Allergen fragments

ABSTRACT

The present invention relates to a peptide derived from the ragweed pollen allergen Amb a (1) and comprising (6 to 50) amino acid residues and pharmaceutical preparations comprising said peptide and uses thereof.

The present invention relates to Amb a 1 derived peptides.

Ragweed (Ambrosia artemisiifolia) and mugwort (Artemisia vulgaris) are important allergenic weeds belonging to the Asteraceae or Compositae plant family. Pollen of mugwort is one of the main causes of allergic reactions in late summer and autumn in Europe and affects about 10-14% of the patients suffering from pollinosis. Ragweed pollen represents the major source of allergenic protein in the United States, with a prevalence of about 50% in atopic 27.10 individuals. In Europe, ragweed allergy is now rapidly increasing particularly in certain areas in France, Italy, Austria, Hungary, Croatia, and Bulgaria. Amb a 1, the major allergen of ragweed and Art v 1, the major allergen from mugwort, respectively, are unrelated proteins. Amb a 1 is an acidic 38 kDa non-glycosylated protein. Natural Amb a 1 undergoes proteolysis during purification and it is cleaved into two chains designated alpha and beta chain. The 26-kDa alpha-chain was reported to associate non-covalently with the 12-kDa beta chain (King et al. Immunochem 11:83-92, 1974). The Amb a 1 two-chain form seems to be immunologically indistinguishable from the full-length molecule (King et al. Arch Biochem Biophys 212:127-135, 1981).

Natural Amb a 1 (nAmb a 1) from ragweed was the first described and isolated allergen (King et al. Biochem 3:458-468, 1964). The cDNA coding for Amb a 1 was isolated from ragweed pollen in 1991 by Rafnar et al. (J. Biol. Chem. 266:1229-1236). But so far, a method to express and purify large amounts of active and correctly folded recombinant Amb a 1 (rAmb a 1) has not been reported.

WO 96/13589 relates to isolated peptides which are derived from Amb a 1 and comprise at least one T-cell epitope.

In the WO 90/11293 the amino acid sequence of Amb a 1 is described. Therein, also peptides of Amb a 1 have been identified which comprise T-cell-epitopes and which are capable of triggering an Ambrosia-specific immune response.

WO 99/34826 relates to methods and means for desensitizing patients by administering a peptide derived from an allergen, which peptide is capable of triggering a T-cell response in an individual.

In Michael J. G. et al. (J. Br. Soc. Aller. Clin. Immunol. 20(6) (1990):669-674) the T-cell response of peptides which are obtained by a protease digestion of Amb a 1 has been examined.

Cardinale E. J. et al. (J. Aller. Clin. Immunol. 107(2001):p 19) relates to the use of MALDI-TOF mass spectrometry for identifying and characterizing allergens.

U.S. Pat. No. 6,335,019 relates i.a., to Amb a 1 peptides capable of provoking a T-cell response against Amb a 1 in an individual.

Griffith et al. (Int. Arch. Aller. Appl. Immunol. 96(1991): 296-304) relates to the sequence polymorphins of Amb a 1 and Amb a 2 family members.

It is an object of the present invention to provide peptides and molecules derived from ragweed pollen allergen Amb a 1 which can be employed in the treatment, prevention or diagnosis of allergies, in particular allergies caused by ragweed pollen allergens.

Therefore, the present invention relates to peptides derived from the ragweed pollen allergen Amb a 1, in particular from Amb a 1.3, consisting of an amino acid sequence selected from the group consisting of SEQ ID No. 12, SEQ ID No. 20, SEQ ID No. 27, SEQ ID No. 28, SEQ ID No. 30, SEQ ID No. 31, SEQ ID No. 33, SEQ ID No. 36, SEQ ID No. 37, SEQ ID No. 38, SEQ ID No. 39, SEQ ID No. 41, SEQ ID No. 42, SEQ ID No. 44, SEQ ID No. 46, SEQ ID No. 47, SEQ ID No. 48, SEQ ID No. 50, SEQ ID No. 51, SEQ ID No. 52, SEQ ID No. 53, SEQ ID No. 59, SEQ ID No. 60, SEQ ID No. 61, SEQ ID No. 67, SEQ ID No. 68, SEQ ID No. 69, SEQ ID No. 77, SEQ ID No. 78, SEQ ID No. 79, SEQ ID No. 80, SEQ ID No. 81, SEQ ID No. 83, SEQ ID No. 86, SEQ ID No. 87, SEQ ID No. 88, SEQ ID No. 89, SEQ ID No. 90, SEQ ID No. 91, SEQ ID No. 93, SEQ ID No. 94, SEQ ID No. 96, SEQ ID No. 97, SEQ ID No. 98, SEQ ID No. 99, SEQ ID No. 100, SEQ ID No. 101, SEQ ID No. 102, SEQ ID No. 107, SEQ ID No. 108, SEQ ID No. 109, SEQ ID No. 110, SEQ ID No. 111, SEQ ID No. 112, SEQ ID No. 114, SEQ ID No. 115, SEQ ID No. 118, SEQ ID No. 119, SEQ ID No. 120, SEQ ID No. 121, SEQ ID No. 122, SEQ ID No. 123, SEQ ID No. 124, SEQ ID No. 125, SEQ ID No. 126, SEQ ID No. 127, SEQ ID No. 128, SEQ ID No. 129, SEQ ID No. 130, SEQ ID No. 131, SEQ ID No. 132, SEQ ID No. 133, SEQ ID No. 134, SEQ ID No. 135, SEQ ID No. 136, SEQ ID No. 137, SEQ ID No. 138, SEQ ID No. 139 and functional equivalents thereof.

It turned out that the peptides of the present invention having an amino acid sequence selected from the group consisting of SEQ ID No. 12, SEQ ID No. 20, SEQ ID No. 27, SEQ ID No. 28, SEQ ID No. 30, SEQ ID No. 31, SEQ ID No. 33, SEQ ID No. 36, SEQ ID No. 37, SEQ ID No. 38, SEQ ID No. 39, SEQ ID No. 41, SEQ ID No. 42, SEQ ID No. 44, SEQ ID No. 46, SEQ ID No. 47, SEQ ID No. 48, SEQ ID No. 50, SEQ ID No. 51, SEQ ID No. 52, SEQ ID No. 53, SEQ ID No. 59, SEQ ID No. 60, SEQ ID No. 61, SEQ ID No. 67, SEQ ID No. 68, SEQ ID No. 69, SEQ ID No. 77, SEQ ID No. 78, SEQ ID No. 79, SEQ ID No. 80, SEQ ID No. 81, SEQ ID No. 83, SEQ ID No. 86, SEQ ID No. 87, SEQ ID No. 88, SEQ ID No. 89, SEQ ID No. 90, SEQ ID No. 91, SEQ ID No. 93, SEQ ID No. 94, SEQ ID No. 96, SEQ ID No. 97, SEQ 10 No. 98, SEQ ID No. 99, SEQ ID No. 100, SEQ ID No. 101, SEQ ID No. 102, SEQ ID No. 107, SEQ ID No. 108, SEQ ID No. 109, SEQ ID No. 110, SEQ ID No. 111, SEQ ID No. 112, SEQ ID No. 114, SEQ ID No. 115, SEQ ID No. 118, SEQ ID No. 119, SEQ ID No. 120, SEQ ID No. 121, SEQ ID No. 122, SEQ ID No. 123, SEQ ID No. 124, SEQ ID No. 125, SEQ ID No. 126, SEQ ID No. 127, SEQ ID No. 128, SEQ ID No. 129, SEQ ID No. 130, SEQ ID No. 131, SEQ ID No. 132, SEQ ID No. 133, SEQ ID No. 134, SEQ ID No. 135, SEQ ID No. 136, SEQ ID No. 137, SEQ ID No. 138 and SEQ ID No. 139, show reactivity with T cells isolated from allergic individuals and, consequently, may be employed in the production of vaccines, especially vaccines for allergies caused by ragweed pollen allergens and allergies cross-reacting to ragweed pollen allergens. In particular the peptides having SEQ ID No. 52, SEQ ID No. 68, SEQ ID No. 86, SEQ ID No. 91 and SEQ ID No. 126 to SEQ ID No. 139 show high T cell reactivity with samples obtained from individuals suffering from ragweed pollen allergy.

A further advantage of the peptides of the present invention is that all of them lack IgE binding activity. Therefore, molecules comprising these peptides do not provoke allergic reactions (e.g. increased release of histamine) when administered to an individual.

For therapeutic purposes peptides derived from allergens do not bind IgE specific for Amb a 1 or bind such IgE to a substantially lesser extent (e.g. at least 100 fold less and more preferably, at least 1000 fold less binding) than the corresponding purified native Amb a 1 or the recombinantly produced beta chain of Amb a 1. If a peptide of the invention is to be used as a diagnostic reagent, it is not necessary that the peptide or protein has reduced IgE binding activity compared to the native Amb a 1 allergen. IgE binding activity of peptides can be determined by, for example, an enzyme linked immunosorbent assay (ELISA) using, for example, sera obtained from an individual (i.e. an allergic individual) that has been previously exposed to the native Amb a 1. Briefly, a peptide to be tested is coated onto wells of a microtiter plate. After washing and blocking the wells, antibody solution consisting of the serum or plasma of an allergic individual who has been exposed to the peptide being tested or the protein from which it was derived is incubated in the wells. The plasma is generally depleted of IgG before incubation. However, the depletion is not necessary if highly specific anti IgE-antibodies are used. Furthermore, allergic individuals who have not undergone specific immunotherapy have in some cases almost no detectable IgG antibodies specific for the allergen in question. A labelled secondary antibody is added to the wells and incubated. The amount of IgE binding is then quantified and compared to the amount of IgE bound by a purified native Amb a 1 protein. Alternatively, the binding activity of a peptide can be determined by Western blot analysis. For example, a peptide to be tested is run on a polyacrylamide gel using SDS-PAGE. The peptide is then transferred to nitrocellulose and subsequently incubated with sera from an allergic subject. After incubation with the labelled secondary antibody, the amount of IgE bound is then determined and quantified.

Another assay which can be used to determine IgE binding activity of a peptide is a competition ELISA assay. Briefly, an IgE antibody pool is generated by combining plasma or serum from ragweed pollen allergic individuals that have been shown by direct ELISA to have IgE reactive with native Amb a 1. This pool is used in ELISA competition assays to compare IgE binding to native Amb a 1 to the peptide tested. IgE binding for the native Amb a 1 protein and the peptide being tested is determined and quantified.

Furthermore, the peptides of the present invention do preferably not result in the release of mediators (e.g. histamines) from mast cells or basophils. To determine whether a peptide which binds IgE results in the release of mediators, a histamine release assay can be performed using standard reagents and protocols. Briefly, a buffered solution of a peptide to be tested is combined with an equal volume of whole heparinized blood from an allergic subject. After mixing and incubation, the cells are pelleted and the supernatants are processed and analyzed using, e.g., a radioimmunoassay to determine the amount of histamine released.

The molecule of the present invention may comprise in any combination more than one peptides of the present invention. These peptides may be conjugated chemically or fused by recombinant technology to each other. Such a molecule may comprise at least two, three, four, five, seven, ten, 15, 20, peptides.

The at least one peptide of the invention can be produced by recombinant DNA techniques in a host cell transformed with a nucleic acid having a sequence encoding such peptide. The isolated peptides of the invention can also be produced by chemical synthesis. Of course it is also possible to produce the peptides by chemical or enzymatic cleavage of the protein allergen.

When a peptide is produced by recombinant techniques, host cells transformed with a nucleic acid of the invention (or the functional equivalent of the nucleic acid having a sequence encoding the peptide (or functional equivalent of the peptide) are cultured in a medium suitable for the cells. Peptides can be purified from cell culture medium, host cells or both using techniques known in the art for purifying peptides and proteins including ion-exchange chromatography, gel filtration chromatography, ultrafiltration, electrophoresis or immunopurification with antibodies specific for the peptide. Isolated peptides of the invention are substantially free of cellular material or culture medium when produced by recombinant DNA techniques or substantially free of chemical precursors or other chemicals when synthesized chemically or free of other materials and reagents when produced by chemical or enzymatic cleavage.

The peptides of the present invention may also be modified by amino acid substitution, deletion or addition. Therefore, the peptides of the present invention comprise at least 7 amino acid residues of the amino acid sequences SEQ ID No. 1 to 139. Also within the present invention are peptides having more than 12 amino acid residues, whereby these additional residues may be derived from the native Amb a 1 molecule and being found adjacent to the peptide in the native Amb a 1 molecule, random amino acids or other peptides or proteins. However, these modified peptides (variants) exhibit similar or even identical properties as the unmodified peptides. In particular the immunogenic properties have to be substantially identical. This means that antibodies directed to these modified peptides are also able to bind to peptides having amino acid sequences SEQ ID No. 1 to 139.

As used herein, a “peptide” refers to an amino acid sequence having fewer amino acid residues than the entire amino acid sequence of the protein from which the peptide was derived. The term “peptide” also refers to any functional equivalents or variants of a peptide or to any fragments or portions of a peptide. “Functional equivalents” of a peptide include peptides having the same or enhanced ability to bind MHC, peptides capable of stimulating the same T cell subpopulations, peptides having the same or increased ability to induce T cell responses such as stimulation (proliferation or cytokine secretion), peptides having at least the same level of reduced IgE binding, and peptides which elicit at least the same minimal level of IgE synthesis stimulating activity as the peptides directly derived from Amb a 1. Minimal IgE stimulating activity refers to IgE synthesis stimulating activity that is less than the amount of IgE production elicited by a purified native ragweed pollen allergen. The peptides and functional equivalents thereof of the present invention consist preferably of 6 to 50, preferably 7 to 45, more preferably 8 to 40, even more preferably 9 to 35, in particular 10 to 30, amino acid residues. “Functional equivalents” of the peptides of the invention may further comprise at the C- and/or N-terminus of said peptides at least one further amino acid residue, which may serve as a linking group (e.g. cysteine) or which may can be found adjacent to the peptide in wild-type Amb a 1.

The term “variant” as used herein refers to an amino acid sequence that differs by one or more amino acid residues from another, usually related polypeptide. The variant may have “conservative” changes, wherein a substituted amino acid has similar structural or chemical properties. One type of conservative amino acid substitutions refer to the interchangeability of residues having similar side chains. For example, a group of amino acids having aliphatic side chains is glycine, alanine, valine, leucine, and isoleucine; a group of amino acids having aliphatic-hydroxyl side chains is serine and threonine; a group of amino acids having amide-containing side chains is asparagine and glutamine; a group of amino acids having aromatic side chains is phenylalanine, tyrosine, and tryptophan; a group of amino acids having basic side chains is lysine, arginine, and histidine; and a group of amino acids having sulfur-containing side chains is cysteine and methionine. Preferred conservative amino acids substitution groups are: valine-leucine-isoleucine, phenylalanine-tyrosine, lysine-arginine, alanine-valine, and asparagine-glutamine. More rarely, a variant may have “non-conservative” changes (for example, replacement of a glycine with a tryptophan). Similar minor variations may also include amino acid deletions or insertions, or both. Preferred variants of the peptides and molecules of the present invention have less than 10%, and preferably less than 5%, and still more preferably less than 2% changes (whether substitutions, deletions, and insertions).

Another aspect of the present invention relates to a peptide derived from the ragweed pollen allergen Amb a 1 and consisting of an amino acid sequence selected from the group consisting of SEQ ID No. 12, SEQ ID No. 20, SEQ ID No. 27, SEQ ID No. 28, SEQ ID No. 30, SEQ ID No. 31, SEQ ID No. 33, SEQ ID No. 36, SEQ ID No. 37, SEQ ID No. 38, SEQ ID No. 39, SEQ ID No. 41, SEQ ID No. 42, SEQ ID No. 44, SEQ ID No. 46, SEQ ID No. 47, SEQ ID No. 48, SEQ ID No. 50, SEQ ID No. 51, SEQ ID No. 52, SEQ ID No. 53, SEQ ID No. 59, SEQ ID No. 60, SEQ ID No. 61, SEQ ID No. 67, SEQ ID No. 68, SEQ ID No. 69, SEQ ID No. 77, SEQ ID No. 78, SEQ ID No. 79, SEQ ID No. 80, SEQ ID No. 81, SEQ ID No. 83, SEQ ID No. 86, SEQ ID No. 87, SEQ ID No. 88, SEQ ID No. 89, SEQ ID No. 90, SEQ ID No. 91, SEQ ID No. 93, SEQ ID No. 94, SEQ ID No. 96, SEQ ID No. 97, SEQ ID No. 98, SEQ ID No. 99, SEQ ID No. 100, SEQ ID No. 101, SEQ ID No. 102, SEQ ID No. 107, SEQ ID No. 108, SEQ ID No. 109, SEQ ID No. 110, SEQ ID No. 111, SEQ ID No. 112, SEQ ID No. 114, SEQ ID No. 115, SEQ ID No. 118, SEQ ID No. 119, SEQ ID No. 120, SEQ ID No. 121, SEQ ID No. 122, SEQ ID No. 123, SEQ ID No. 124, SEQ ID No. 125, SEQ ID No. 126, SEQ ID No. 127, SEQ ID No. 128, SEQ ID No. 129, SEQ ID No. 130, SEQ ID No. 131, SEQ ID No. 132, SEQ ID No. 133, SEQ ID No. 134, SEQ ID No. 135, SEQ ID No. 136, SEQ ID No. 137, SEQ ID No. 138 and SEQ ID No. 139.

Another aspect of the present invention relates to a molecule comprising at least one peptide of the present invention and at least one second peptide derived from an immunogen other than Amb a 1.

The molecule of the present invention may be conjugated, bound chemically or fused to one or more other peptides which are not derived from Amb a 1. Such a molecule may be employed, for instance, as a vaccine inducing an immune response against a ragweed pollen allergen peptide of the present invention and said second immunogen (e.g. of bacterial or viral origin).

In order to elicit antibodies against small molecules (hapten) like the peptides of the present invention these small molecules may be linked (e.g. conjugated) to a carrier. This linkage makes the hapten immunogenic, this means antibodies are generated after injection into an individual. The binding of the hapten to a carrier protein is often covalent, but it can be ionic or be effected through a chemical component bridging the hapten and the carrier. The carrier is typically a protein, but it can also contain sugar and fat in mono- or polymer form.

The immunogen according to the present invention is preferably an allergen, preferably selected from the group consisting of Amb a 2, Amb a 3, Amb a 5, Amb a 6, Amb a 7, Amb a 8, Amb a 9, Amb a 10, Amb t 5, Art v 1, Art v 2, Art v 3, Art v 4, Art v 5, Art v 6, Hel a 1, Hel a 2, Hel a 3, Mer a 1, Che a 1, Che a 2, Che a 3, Sal k 1, Cat r 1, Pla l 1, Hum j 1, Far j 1, Par j 2, Par j 3, Par o 1, Cyn d 1, Cyn d 7, Cyn d 12, Cyn d 15, Cyn d 22w, Cyn d 23, Cyn d 24, Dac g 1, Dac g 2, Dac g 3, Dac g 5, Fes p 4w, Hol l 1, Lol p 1, Lol p 2, Lol p 3, Lol p 5, Lol p 11, Pha a 1, Phl p 1, Phl p 2, Phl p 4, Phl p 5, Phl p 6, Phl p 11, Phl p 12, Phl p 13, Poa p 1, Poa p 5, Sor h 1, Pho d 2, Aln g 1, Bet v 1, Bet v 2, Bet v 3, Bet v 4, Bet v 6, Bet v 7, Car b 1, Cas s 1, Cas s 5, Cas s 8, Cor a 1, Cor a 2, Cor a 8, Cor a 9, Cor a 10, Cor a 11, Que a 1, Fra e 1, Lig v 1, Ole e 1, Ole e 2, Ole e 3, Ole e 4, Ole e 5, Ole e 6, Ole e 7, Ole e 8, Ole e 9, Ole e 10, Syr v 1, Cry j 1, Cry j 2, Cup a 1, Cup s 1, Cup s 3w, Jun a 1, Jun a 2, Jun a 3, Jun o 4, Jun s 1, Jun v 1, Pla a 1, Pla a 2, Pla a 3, Aca s 13, Blo t 1, Blo t 3, Blo t 4, Blo t 5, Blo t 6, Blo t 10, Blo t 11, Blo t 12, Blo t 13, Blo t 19, Der f 1, Der f 2, Der f 3, Der f 7, Der f 10, Der f 11, Der f 14, Der f 15, Der f 16, Der f 17, Der f 18w, Der m 1, Der p 1, Der p 2, Der p 3, Der p 4, Der p 5, Der p 6, Der p 7, Der p 8, Der p 9, Der p 10, Der p 11, Der o 14, Der p 20, Der p 21, Eur m 2, Eur m 14, Gly d 2, Lep d 1, Lep d 2, Lep d 5, Lep d 7, Lep d 10, Lep d 13, Tyr p 2, Tyr p 13, Bos d 2, Bos d 3, Bos d 4, Bos d 5, Bos d 6, Bos d 7, Bos d 8, Can f 1, Can f 2, Can f 3, Can f 4, Equ c 1, Equ c 2, Equ c 3, Equ c 4, Equ c 5, Fel d 1, Fel d 2, Fel d 3, Fel d 4, Fel d 5w, Fel d 6w, Fel d 7w, Cav p 1, Cav p 2, Mus m 1, Rat n 1, Alt a 1, Alt a 3, Alt a 4, Alt a 5, Alt a 6, Alt a 7, Alt a 8, Alt a 10, Alt a 12, Alt a 13, Cla h 2, Cla h 5, Cla h 6, Cla h 7, Cla h 8, Cla h 9, Cla h 10, Cla h 12, Asp fl 13, Asp f 1, Asp f 2, Asp f 3, Asp f 4, Asp f 5, Asp f 6, Asp f 7, Asp f 8, Asp f 9, Asp f 10, Asp f 11, Asp f 12, Asp f 13, Asp f 15, Asp f 16, Asp f 17, Asp f 18, Asp f 22w, Asp f 23, Asp f 27, Asp f 28, Asp f 29, Asp n 14, Asp n 18, Asp n 25, Asp o 13, Asp o 21, Pen b 13, Pen b 26, Pen ch 13, Pen ch 18, Pen ch 20, Pen c 3, Pen c 13, Pen c 19, Pen c 22w, Pen c 24, Pen o 18, Fus c 1, Fus c 2, Tri r 2, Tri r 4, Tri t 1, Tri t 4, Carid a 1, Cand a 3, Cand b 2, Psi c 1, Psi c 2, Cop c 1, Cop c 2, Cop c 3, Cop c 5, Cop c 7, Rho m 1, Rho m 2, Mala f 2, Mala f 3, Mala f 4, Mala s 1, Mala s 5, Mala s 6, Mala s 7, Mala s 8, Mala s 9, Mala s 10, Mala s 11, Mala s 12, Mala s 13, Epi p 1, Aed a 1, Aed a 2, Api m 1, Api m 2, Api m 4, Api m 6, Api m 7, Bom p 1, Bom p 4, Bla g 1, Bla g 2, Bla g 4, Bla g 5, Bla g 6, Bla g 7, Bla g 8, Per a 1, Per a 3, Per a 6, Per a 7, Chi k 10, Chi t 1-9, Chi t 1.01, Chi t 1.02, Chi t 2.0101, Chi t 2.0102, Chi t 3, Chi t 4, Chi t 5, Chi t 6.01, Chi t 6.02, Chi t 7, Chi t 8, Chi t 9, Cte f 1, Cte f 2, Cte f 3, Tha p 1, Lep s 1, Dol m 1, Dol m 2, Dol m 5, Dol a 5, Pol a 1, Pol a 2, Pol a 5, Pol d 1, Pol d 4, Pol d 5, Pol e 1, Pol e 5, Pol f 5, Pol g 5, Pol m 5, Vesp c 1, Vesp c 5, Vesp m 1, Vesp m 5, Ves f 5, Ves g b, Ves m 1, Ves m 2, Ves m 5, Ves p 5, Ves s 5, Ves vi 5, Ves v 1, Ves v 2, Ves v 5, Myr p 1, Myr p 2, Sol g 2, Sol g 4, Sol i 2, Sol i 3, Sol i 4, Sol s 2, Tria p 1, Gad c 1, Sal s 1, Bos d 4, Bos d 5, Bos d 6, Bos d 7, Bos d 8, Gal d 1, Gal d 2, Gal d 3, Gal d 4, Gal d 5, Met e 1, Pen a 1, Pen i 1, Pen m 1, Pen m 2, Tod p 1, Hel as 1, Hal m 1, Ran e 1, Ran e 2, Bra j 1, Bra n 1, Bra o 3, Bra r 1, Bra r 2, Hor v 15, Hor v 16, Hor v 17, Hor v 21, Sec c 20, Tri a 18, Tri a 19, Tri a 25, Tri a 26, Zea m 14, Zea m 25, Ory s 1, Api g 1, Api g 4, Api g 5, Dau c 1, Dau c 4, Cor a 1.04, Cor a 2, Cor a 8, Fra a 3, Fra a 4, Mal d 1, Mal d 2, Mal d 3, Mal d 4, Pyr c 1, Pyr c 4, Pyr c 5, Pers a 1, Pru ar 1, Pru ar 3, Pru av 1, Pru av 2, Pru av 3, Pru av 4, Pru d 3, Pru du 4, Pru p 3, Pru p 4, Aspa o 1, Cro s 1, Cro s 2, Lac s 1, Vit v 1, Mus xp 1, Ana c 1, Ana c 2, Cit l 3, Cit s 1, Cit s 2, Cit s 3, Lit c 1, Sin a 1, Gly m 1, Gly m 2, Gly m 3, Gly m 4, Vig r 1, Ara h 1, Ara h 2, Ara h 3, Ara h 4, Ara h 5, Ara h 6, Ara h 7, Ara h 8, Len c 1, Len c 2, Pis s 1, Pis s 2, Act c 1, Act c 2, Cap a 1w, Cap a 2, Lyc e 1, Lyc e 2, Lyc e 3, Sola t 1, Sola t 2, Sola t 3, Sola t 4, Ber e 1, Ber e 2, Jug n 1, Jug n 2, Jug r 1, Jug r 2, Jug r 3, Ana o 1, Ana o 2, Ana o 3, Ric c 1, Ses i 1, Ses i 2, Ses i 3, Ses i 4, Ses i 5, Ses i 6, Cuc m 1, Cuc m 2, Cuc m 3, Ziz m 1, Ani s 1, Ani s 2, Ani s 3, Ani s 4, Arg r, Asc s 1, Car p 1, Den n 1, Hev b 1, Hev b 2, Hev b 3, Hev b 4, Hev b 5, Hev b 6.01, Hev b 6.02, Hev b 6.03, Hev b 7.01, Hev b 7.02, Hev b 8, Hev b 9, Hev b 10, Hev b 11, Ilev b 12, Hev b 13, Hom s 1, Hom s 2, Hom s 3, Hom s 4, Hom s 5 and Trip s 1.

It is particularly preferred to fuse and/or conjugate the peptides of the present invention derived from ragweed pollen allergen Amb a 1 to other allergens or peptides derived from said allergens. Such a fusion protein/polypeptide/peptide or conjugate is useful when used in a vaccine or in diagnosis.

Another aspect of the present invention relates to a nucleic acid molecule encoding a peptide or a molecule according to the present invention.

The nucleic acid molecule of the present invention may be employed, e.g., for the recombinant production of the peptides/polypeptides/proteins encoded by said nucleic acid molecule. Furthermore, they may also be used for therapeutic aspects (e.g. gene therapy, cell therapy).

Another aspect of the present invention relates to a vector comprising a nucleic acid molecule according to the present invention.

The nucleic acid molecule of the present invention may be introduced into a vector. The vector may be used for the recombinant production of the peptides and molecules of the present invention or for therapeutic aspects.

“Vector”, as used herein, refers to a plasmid, cosmid and viral and phage DNA. A plasmid comprising a nucleic acid molecule according to the present invention may contain next to said molecule, e.g., an origin of replication, selection markers (e.g. antibiotic resistance markers, auxotrophic markers), a multiple cloning site, a promoter region operably linked to said molecule and/or sequence stretches for the homologue integration of the vector or parts thereof into the genome of a host.

Preferably, the vector of the present invention further comprises a promoter operably linked to said nucleic acid molecule, thus resulting in an expression cassette.

The expression cassette of the present invention comprises a promoter and a nucleic acid molecule encoding for a peptide of the present invention. The promoter is preferably positioned at the 5′-end (upstream) of the nucleic acid molecule of the present invention. The promoter to be used in the expression cassette may be any one, provided that the promoter can be controlled by the respective host.

A further aspect of the present invention relates to a vaccine formulation comprising at least one molecule and/or at least one peptide according to the present invention.

The peptide and/or molecule of the present invention comprising at least one peptide derived from the ragweed pollen allergen Amb a 1 and consisting of an amino acid sequence selected from the group consisting of SEQ ID No. 1 to 139 can be used in a vaccine formulation. Since these peptides are able to provoke a T cell response against the ragweed pollen allergen Amb a 1 the vaccine formulation may be used for the desensitization, prevention or treatment of ragweed pollen allergies and allergies cross-reacting with ragweed pollen allergens (e.g. mugwort pollen). Due to the lack of IgE binding activity the peptides are in particular advantageous when used in a vaccine, because no or substantially no allergic reaction is provoked by said vaccine. The vaccine formulation of the present invention may comprise at least one, preferably at least two, more preferably at least three, peptides of the present invention.

Administration of the therapeutic compositions of the present invention to an individual to be desensitized can be carried out using known procedures at dosages and for periods of time effective to reduce sensitivity (i.e. reduce the allergic response) of the individual to the allergen. Effective amounts of the therapeutic compositions will vary according to factors such as the degree of sensitivity of the individual to Amb a 1, the age, sex and weight of the individual and the ability of the protein or fragment thereof to elicit an antigenic response in the individual. The active compound (i.e. protein or fragment thereof) may be administered in a convenient manner such as by injection (subcutaneous, intravenous, etc.), oral administration, inhalation, transdermal application, or rectal administration. Depending on the route of administration, the active compound may be coated within a material to protect the compound from the action of enzymes, acids and other natural conditions which may inactivate the compound (see below). For example, preferably about 0.05 μg-1000 μg, more preferably from about 0.1-100 μg of active compound (i.e. protein or fragment thereof) per dosage unit may be administered by injection. Dosage regimen may be adjusted to provide the optimum therapeutic response. For example, several divided doses may be administered daily or the dose may be proportionally reduced as indicated by the exigencies of the therapeutic situation.

Of course, it is also possible and in the scope of the present invention providing an antibody bound to a peptide or molecule according to the present invention which may also be used in vaccine formulations.

Antibodies according to the present invention include, but are not limited to, polyclonal, monoclonal, multispecific, humanized or chimeric antibodies, single chain antibodies, Fab fragments, F(ab′) fragments and epitope-binding fragments of any of the above. Furthermore, antibodies are considered as being immunoglobulin molecules and immunologically active portions of immunoglobulin molecules, i.e., molecules that contain an antigen binding site that immunospecifically binds an antigen.

The immunoglobulin molecules of the invention are preferably of the types IgG, IgM, IgD, IgA and IgY, class (e.g., IgG1, IgG2, IgG3, IgG4, IgA1 and IgA2) or subclass of immunoglobulin molecule.

Polyclonal antibodies can be prepared by administering a polypeptide of the invention, preferably using an adjuvant, to a non-human mammal and collecting the resultant antiserum. Improved titres can be obtained by repeated injections over a period of time. There is no particular limitation to the species of mammals which may be used for eliciting antibodies; it is generally preferred to use rabbits or guinea pigs, but horses, cats, dogs, goats, pigs, rats, cows, sheep, camels etc., can also be used. In the production of antibodies, a definite amount of immunogen of the invention is e.g. diluted with physiological saline solution to a suitable concentration and the resulting diluted solution is mixed with, e.g. complete Freund's adjuvant to prepare a suspension or with mineral gels such as aluminum hydroxide, surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanins, dinitrophenol, and potentially useful human adjuvants such as BCG (bacille Calmette-Guerin) and corynebacterium parvum. The suspensions and mixtures are administered to mammals, e.g. intraperitoneally, e.g. to a rabbit, using from about 50 μg to about 2500 μg polypeptide of the invention per administration. The suspension is preferably administered about every two weeks over a period of up to about 2-3 months, preferably about 1 month, to effect immunization. Antibody is recovered by collecting blood from the immunized animal after the passage of 1 to 2 weeks subsequently to the last administration, centrifuging the blood and isolating serum from the blood.

Monoclonal antibodies may e.g. be of human or murine origin. Murine monoclonal antibodies may be prepared by the method of Köhler and Milstein (Köhler, G. and Milstein, C., Nature 256 (1975) 495), e.g. by fusion of spleen cells of hyperimmunized mice with an appropriate mouse myeloma cell line.

A chimeric antibody is a molecule in which different portions of the antibody are derived from different animal species, such as antibodies having a variable region derived from a murine monoclonal antibody and a human immunoglobulin constant region. Methods for producing chimeric antibodies are known in the art. See e.g., Morrison, Science 229:1202 (1985); Oi et al., BioTechniques 4:214 (1986); Gillies et al., (1989) J. Immunol. Methods 125:191-202; U.S. Pat. No. 5,807,715; U.S. Pat. No. 4,816,567 and U.S. Pat. No. 4,816,397.

Humanized antibodies are antibody molecules from non-human species antibody that binds the desired antigen having one or more complementarity determining regions (CDRs) from the non-human species and framework regions from a human immunoglobulin molecule. Often, framework residues in the human framework regions will be substituted with the corresponding residue from the CDR donor antibody to alter, preferably improve, antigen binding. These framework substitutions are identified by methods well known in the art, e.g., by modelling of the interactions of the CDR and framework residues to identify framework residues important for antigen binding and sequence comparison to identify unusual framework residues at particular positions (see, e.g., Queen et al., U.S. Pat. No. 5,585,089; Riechmann et al., Nature 332:323 (1988)). Antibodies can be humanized using a variety of techniques known in the art including, for example, CDR-grafting (EP 239,400; WO 91/09967; U.S. Pat. No. 5,225,539; U.S. Pat. No. 5,530,101; and U.S. Pat. No. 5,585,089), veneering or resurfacing (EP 592,106; EP 519,596; Padlan, Molecular Immunology 28(4/5):489-498 (1991); Studnicka et al., Protein Engineering 7(6):805-814 (1994); Roguska. et al., PNAS 91:969-913 (1994)), and chain shuffling (U.S. Pat. No. 5,565,332).

The antibodies according to the present invention may advantageously be used for passive immunisation of an individual suffering from an allergy, in particular from house dust mite allergy. For passive immunisation the antibody is preferably an IgG or a derivative thereof (e.g. chimeric or humanized antibody). Furthermore this antibody may also be used for desensibilisation of an individual.

The vaccine formulation of the present invention further comprises at least one pharmaceutical acceptable adjuvant, excipient and/or carrier.

Pharmaceutically acceptable carriers preferably used are physiological saline, vegetable oils, mineral oil, aqueous sodium caroboxymethyl cellulose or aqueous polyvinylpyrrolidone. Suitable adjuvants include, but are not limited to: surface active substances, e.g., hexadecylamine, octadecylamine, octadecyl amino acid esters, lysolecithin, dimethyl-dioctadecylammonium bromide, methoxyhexadecylgylcerol, and pluronic polyols; polyamines, e.g., pyran, dextran-sulfate, poly IC, carbopol; peptides, e.g., muramyl dipeptide, dimethylglycine, tuftsin; oil emulsions; and mineral gels, e.g., aluminum hydroxide, aluminum phosphate, etc. and immune stimulating complexes. The adjuvant may be, for example, alum or a composition containing a vegetable oil, isomannide monooleate and aluminum mono-stearate. Other preferred adjuvants include microparticles or beads of biocompatible matrix materials. The molecules of the present invention may be incorporated into microparticles or microcapsules to prolong the exposure of the antigenic material to the individual and hence protect said individual against infection for long periods of time. The immunogen may also be incorporated into liposomes or conjugated to polysaccharides and/or other polymers for use in a vaccine formulation.

Also part of this invention is a composition that comprises the molecules, in particular the peptides, of this invention and a carrier, preferably a biologically-acceptable carrier, and more preferably a pharmaceutically-acceptable carrier. Typical carriers are aqueous carriers such as water, buffered aqueous solutions, aqueous alcoholic mixtures, and the like. Compositions comprising carriers that are for pharmaceutical use, particularly for use in humans, comprise a carrier that is pharmaceutically-acceptable. Examples of such carriers are known in the art.

Typically, such vaccines are prepared as injectables: either as liquid solutions or suspensions, solid forms suitable for solution in, or suspension in, liquid prior to injection may also be prepared. The vaccine may be administered to a target animal by any convenient route, such as subcutaneously, intraperitoneally, intramuscularly, intradermally, intravenously, orally, intranasally or intramammarily, in the presence of a physiologically acceptable diluent. The antigens may be administered in a single dose or in a plurality of doses. The vaccine of the present invention may be stored under refrigeration or in frozen or lyophilized form. The vaccine is administered to an individual in an amount effective to elicit a protective immune response as compared to a control. The effective amount will vary, e.g., with the age and size and may be readily determined by the practitioner skilled in the art. Suitable regimes for initial administration and booster shots will also be variable, but may be typified by an initial administration followed by subsequent inoculations or other administrations.

The vaccine formulation of the present invention contains at least one molecule comprising a peptide selected from the group consisting of SEQ ID No. 12, SEQ ID No. 20, SEQ ID No. 27, SEQ ID No. 28, SEQ ID No. 30, SEQ ID No. 31, SEQ ID No. 33, SEQ ID No. 36, SEQ ID No. 37, SEQ ID No. 38, SEQ ID No. 39, SEQ ID No. 41, SEQ ID No. 42, SEQ ID No. 44, SEQ ID No. 46, SEQ ID No. 47, SEQ ID No. 48, SEQ ID No. 50, SEQ ID No. 51, SEQ ID No. 52, SEQ ID No. 53, SEQ ID No. 59, SEQ ID No. 60, SEQ ID No. 61, SEQ ID No. 67, SEQ ID No. 68, SEQ ID No. 69, SEQ ID No. 77, SEQ ID No. 78, SEQ ID No. 79, SEQ ID No. 80, SEQ ID No. 81, SEQ ID No. 83, SEQ ID No. 86, SEQ ID No. 87, SEQ ID No. 88, SEQ ID No. 89, SEQ ID No. 90, SEQ ID No. 91, SEQ ID No. 93, SEQ ID No. 94, SEQ ID No. 96, SEQ ID No. 97, SEQ ID No. 98, SEQ ID No. 99, SEQ ID No. 100, SEQ ID No. 101, SEQ ID No. 102, SEQ ID No. 107, SEQ ID No. 108, SEQ ID No. 109, SEQ ID No. 110, SEQ ID No. 111, SEQ ID No. 112, SEQ ID No. 114, SEQ ID No. 115, SEQ ID No. 118, SEQ ID No. 119, SEQ ID No. 120, SEQ ID No. 121, SEQ ID No. 122, SEQ ID No. 123, SEQ ID No. 124, SEQ ID No. 125, SEQ ID No. 126, SEQ ID No. 127, SEQ ID No. 128, SEQ ID No. 129, SEQ ID No. 130, SEQ ID No. 131, SEQ ID No. 132, SEQ ID No. 133, SEQ ID No. 134, SEQ ID No. 135, SEQ ID No. 136, SEQ ID No. 137, SEQ ID No. 138 and SEQ ID No. 139.

In a particular preferred embodiment of the present invention the vaccine formulation comprises at least one peptide selected from the group consisting of SEQ ID No. 52, SEQ ID No. 68, SEQ ID No. 86, SEQ. ID No. 91, and SEQ ID No. 126-SEQ ID No. 139, wherein a further preferred embodiment of the formulation comprises at least one peptide consisting of an amino acid sequence selected from the group consisting of SEQ ID No. 52 and SEQ ID No. 137 to 139. In particular, these molecules show a high T cell reactivity in patients suffering from ragweed allergy (the peptides are recognized by more than 90% of allergic individuals sensitized to ragweed allergies). Furthermore, these molecules/peptides may be formulated alone or in any combination in one single formulation. Thus the vaccine formulation may comprise at least two, preferably at least three, of the peptides selected from the group consisting of SEQ ID No. 52, SEQ ID No. 68, SEQ ID No. 86, SEQ ID No. 91, and SEQ ID No. 126-SEQ ID No. 139, preferably selected from the group consisting of SEQ ID No. 52 and SEQ ID No. 137 to 139. Particular preferred combinations of the peptides are: SEQ ID No. 52 and SEQ ID No. 137; SEQ ID No. 52 and SEQ ID No. 138; SEQ ID No. 52 and SEQ ID No. 139; SEQ ID No. 137 and SEQ ID No. 138; SEQ ID No. 137 and SEQ ID No. 139; SEQ ID No. 52, SEQ ID No. 137 and SEQ ID No. 138; SEQ ID No. 52, SEQ ID No. 138 and SEQ ID No. 139; SEQ ID No. 52, SEQ ID No. 137 and SEQ ID No. 139; SEQ ID No. 137, SEQ ID No. 138 and SEQ ID No. 139; SEQ ID No. 52, SEQ ID No. 137, SEQ ID No. 138 and SEQ ID No. 139.

Yet another aspect of the present invention relates to the use of a peptide and/or a molecule according to the present invention for the manufacture of a vaccine formulation as outlined above.

The vaccine formulation is used for preventing or treating a ragweed pollen allergy in an individual, in particular an allergy caused by Amb a 1, or an allergy cross-reacting with a ragweed pollen allergy.

Another aspect of the present invention relates to the use of a molecule as disclosed herein for diagnosing a ragweed allergy in an individual or the sensitivity of an individual to a ragweed pollen allergen, in particular to Amb a 1.

The molecules of the present invention, in particular the peptides of the present invention, may be used also for diagnostic purposes. Molecules and peptides of the present invention can be used for detecting and diagnosing ragweed allergy or an allergy cross-reacting with Amb a 1. For example, this could be done by combining blood or blood products obtained from an individual to be assessed for sensitivity to ragweed allergy with an isolated antigenic peptide or peptides of Amb a 1 or isolated Amb a 1 alpha or beta chain, under conditions appropriate for binding components in the blood (e.g., antibodies, T-cells, B-cells) with the peptide(s) or protein and determining the extent to which such binding occurs. Other diagnostic methods for allergic diseases which the peptides of the present invention can be used include radio-allergensorbent test (RAST), paper radioimmunosorbent test (PRIST), enzyme linked immunosorbent assay (ELISA), radioimmunoassays (RIA), immuno-radiometric assays (IRMA), luminescence immunoassays (LIA), histamine release assays and IgE immunoblots.

A further aspect of the present invention relates to a method for diagnosing the sensitivity of an individual to a ragweed pollen allergen, in particular to Amb a 1, comprising the steps:

-   -   providing a sample of an individual containing mast cells or         basophils and/or antibodies, in particular antibodies of the IgE         class,     -   contacting said sample with a molecule/peptide according to the         present invention     -   determining the amount of histamine released from the mast cells         or basophils upon contact with said molecule and/or determining         the amount of ragweed pollen allergen specific antibodies in the         sample, and     -   diagnosing the sensitivity of an individual to a ragweed pollen         allergen, in particular to Amb a 1, if the amount of histamine         released and/or the amount of ragweed pollen allergen specific         antibodies in the sample is increased compared to a sample         obtained from an individual not suffering from a ragweed pollen         allergy or an allergy exhibiting cross-reactivity with ragweed         pollen allergy.

The sample used in the method according to the present invention is preferably a blood, tear, saliva or nasal secretion sample.

Further aspects of the present invention relate to the isolated alpha chain of Amb a 1.3 consisting of amino acid sequence SEQ ID No. 142 (PILRQASDGD TINVAGSSQI WIDHCSLSKS FDGLVDVTLG STHVTISNCK FTQQSKAILL GADDTHVQDK GMLATVAFNM FTDNVDQRMP RCRFGFFQVV NNNYDRWGTY AIGGSSAPTI LCQGNRFLAP DDQIKKNVLA RTGTGAAESM AWNWRSDKDL LENGAIFVTS GSDPVLTPVQ SAGMIPAEPG EAAIKLTSSA GVLSCRPGAP C) or SEQ ID No. 143 (VLPGGMIKSN DGPPILRQAS DGDTINVAGS SQIWIDHCSL SKSFDGLVDV TLGSTHVTIS NCKFTQQSKA ILLGADDTHV QDKGMLATVA FNMFTDNVDQ RMPRCRFGFF QVVNNNYDRW GTYAIGGSSA PTILCQGNRF LAPDDQIKKN VLARTGTGAA ESMAWNWRSD KDLLENGAIF VTSGSDPVLT PVQSAGMIPA EPGEAAIKLT SSAGVLSCRP GAPC) and to an isolated beta chain of Amb a 1.3 consisting of amino acid sequence SEQ ID No. 144 (AEGVGEILPS VNETRSLQAC EAYNIIDKCW RGKADWENNR QALADCAQGF AKGTYGGKWG DVYTVTSNLD DDVANPKEGT LRFAAAQNRP LWIIFKNDMV INLNQELVVN SDKTIDGRGV KVEIINGGLT LMNVKNIIIH NINIHDVKVL PGGMIKSNDG P) or SEQ ID No. 145 (AEGVGEILPS VNETRSLQAC EAYNIIDKCW RGKADWENNR QALADCAQGF AKGTYGGKWG DVYTVTSNLD DDVANPKEGT LRFAAAQNRP LWIIFKNDMV INLNQELVVN SDKTIDGRGV KVEIINGGLT LMNVKNIIIH NINIHDVK).

Amb a 1 can substantially be divided into two fragments, an alpha chain (SEQ ID No. 142 or SEQ ID No. 143) and a beta chain (SEQ ID No. 144). It surprisingly turned out that both chains exhibit different immunological properties. Whilst the alpha chain of Amb a 1 shows low IgE reactivity the beta chain contains most of the IgE epitopes of Amb a 1.

Yet another aspect of the present invention relates to a pharmaceutical preparation comprising an isolated alpha chain of Amb a 1.3 and/or an isolated beta chain of Amb a 1.3 according to the present invention.

Another aspect of the present invention relates to the use of an isolated alpha chain of Amb a 1.3 and/or an isolated beta chain of Amb a 1.3 according to the present invention for the manufacture of a medicament for the treatment of a ragweed pollen allergy in an individual, in particular an allergy caused by Amb a 1, or an allergy cross-reacting with a ragweed pollen allergy.

A further aspect of the present invention relates to the use of an isolated alpha chain of Amb a 1.3 and/or an isolated beta chain of Amb a 1.3 according to the present invention for diagnosing a ragweed allergy in an individual or the sensitivity of an individual to a ragweed pollen allergen, in particular to Amb a 1, or an allergy cross-reacting with a ragweed pollen allergy.

The present invention is further illustrated by the following figures and examples, however, without being restricted thereto.

FIG. 1 shows the purification of rAmb a 1.3 with Nickel Chelate Chromtography (NCC) in 8 M Urea. Samples were analyzed with SDS-PAGE/Coomassie staining. Purified fractions showed extensive aggregation.

FIG. 2 shows IgE dot-blot analysis of recombinant Amb a 1.3. E. coli-produced rAmb a 1.3 was purified as described above and dotted on nitrocellulose membranes. Sera from 17 ragweed pollen allergic patients (1-17) were tested and showed very weak or no IgE reactivity with rAmb a 1.3. The same patients showed strong IgE reactivity with nAmb a 1.

FIG. 3 shows TCL stimulated with purified natural Amb a 1 or rAmb a 1.3 at different concentrations. The values of the optimum concentrations are shown. N=13; Pearson correlation coefficient: 0.979** (p<0.01) or Spearman's rho: 0.912**.

FIG. 4 shows examples of allergen titrations in TCL proliferation assays—natural versus recombinant allergens (different lots of rAmb a 1.3, lots L1-L4). STA and OPO are TCL from 2 different ragweed allergic patients, respectively.

FIG. 5 shows similar cytokine production induced by ragweed extract and rAmb a 1.3 in TCL.

FIG. 6 shows comparable cytokine production induced by natural and rAmb a 1.3 in TCL and TCC.

FIG. 7 shows TCL induced with natural or rAmb a 1.3 recognize similar T cell epitopes.

FIG. 8 shows relevant T cell activating regions of Amb a 1.3. Percentage of patients recognizing each epitope was separately analyzed for stimulation indexes higher than 3 (SI>3) and 5 (SI>5), respectively.

FIG. 9 shows an IgE immunoblot of purified nAmb a 1. nAmb a 1 was separated by SDS-PAGE, and electroblotted onto PVDF membrane. Membrane strips were incubated with sera from ragweed pollen allergic patients (lanes 1-29) or with serum from a non-allergic donor (lane C). Bound IgE was detected with ¹²⁵I-labeled goat anti-human IgE. Ragweed pollen-sensitized patients were recruited in Austria (lanes 1-13) or in Italy (lanes 14-29).

FIG. 10 shows a Coomassie staining of purified natural Amb a 1 after SDS-PAGE and electroblotting onto a PVDF membrane. The bands corresponding to unprocessed nAmb a 1, alpha and beta chains were subjected to Edman-degradation to obtain the N-terminal sequences.

FIG. 11 shows the N-terminal sequence of unprocessed natural Amb a 1 (nAmb a 1, see FIG. 10) and alignment with deduced amino acid sequences of Amb a 1 isoforms.

FIG. 12 shows the N-Terminal sequence of natural Amb a 1 (nAmb a 1, see FIG. 10) alpha chain and alignment with deduced amino acid sequences of Amb a 1 isoforms.

FIG. 13 shows the N-terminal sequence of natural Amb a 1 (nAmb a 1, see FIG. 10) beta chain and alignment with deduced amino acid sequences of Amb a 1 isoforms.

FIG. 14 shows deduced amino acid sequences of Amb a 1 isoforms and their putative alpha and beta chains. Isoforms Amb a 1.1, Amb a 1.2, Amb a 1.3, Amb a 1.4 and Amb a 2 were published (Rafnar et al., J. Biol. Chem. 266: 1229-1236, 1991) and patented (U.S. Pat. No. 5,776,761). The R2 clone was isolated in the laboratory by immunoscreening of a ragweed pollen cDNA pollen with anti-Amb a 1 affinity purified rabbit antibodies and is identical to Amb a 1.3 at the protein level. Letters underlined, predicted signal peptide using the algorithm SignalP (http://www.cbs.dtu.dk/services/SignalP/). In italicized letters, putative beta chain sequence based on N-terminal sequencing and mass measurement of natural Amb a 1. Italicized and underlined, putative alpha chain sequence based on N-terminal sequencing and mass measurement of natural Amb a 1 (FIGS. 10-13; Table 4). N-terminal sequence analysis showed that sequences in bold letters were proteolytically removed in the purified natural Amb a 1 preparation.

FIG. 15 shows a sequence alignment of Amb a 1 isoforms. Amb a 1.1, Amb a 1.2, Amb a 1.3, and Amb a 2 were previously cloned, sequenced and published (Rafnar et al., J. Biol. Chem. 266: 1229-1236, 1991). Sequence alignment was generated using the software Clustalw (http://npsa-pbil.ibcp.fr/cqi-bin/npsa_automat.pl?page=npsa_clustalw.html). The complete deduced amino acid sequences (including signal peptide) given in FIG. 14 were used for the alignment.

FIG. 16 shows deduced amino acid sequence of Amb a 1.3 (R2 clone) and chains. (a) Putative alpha and beta chains based on the information from N-terminal sequencing and mass spectrometry of purified natural Amnb a 1 (see FIGS. 10-13; Table 4). (b) the first construct made in the lab to produce recombinant alpha and beta chains of Amb a 1.3. The expression of the chains was better than full-length Amb a 1.3 but low yields were obtained. In addition, the alpha chain excluded an important T cell reactive domain (boxed, aa 178-189). (c) modified (version 1) alpha and beta chains of Amb a 1.3 designed to include in the alpha chain the T cell epitope corresponding to amino acids 178-189. (d) modified (version 2) alpha and beta chains of Amb a 1.3 designed to include in the alpha chain the T cell epitope corresponding to amino acids 178-189 and to exclude in the beta chain the first 20 amino acids at the N-terminus, which were shown to be proteolytically removed in natural Amb a 1.

FIG. 17 shows the expression of Amb a 1.3 modified (version 1) alpha and beta chains in E. coli strains BL21 and Rosetta-gami B (DE3)pLysS.

FIG. 18 shows SDS-PAGE and Coomassie staining of modified (version 1) Amb a 1.3 alpha and beta chains after affinity purification on nickel column. High yields of modified alpha and beta chains were obtained using E. coli strain Rosetta-gami B (DE3)pLysS (Novagen). The purified chains were soluble and did not show any tendency to aggregate, which was an acute problem with the full-length Amb a 1.3 allergen.

FIG. 19 shows Human IgE ELISA of purified natural Amb a 1 and modified (version 1) alpha chain of Amb a 1.3

FIG. 20 shows proliferation of an Amb a 1-specific TCL with modified (version 1) alpha and beta chains of Amb a 1.3. Natural Amb a 1, different concentrations of full-length rAmb a 1.3, rAlpha and beta chains were used as stimulants. TCL was initiated with rAmb a 1.3 (Amb).

FIG. 21 shows proliferative responses of 2 Amb a 1-specific TCL using full-length rAmb a 1.3, and modified (version 1) alpha and beta chains of Amb a 1.3. TCL were initiated either with rAmb a 1.3 (Amb) or with ragweed pollen extract (RW).

FIG. 22 shows 26 identified relevant T cell activating regions in Amb a 1.3. 17/26 epitopes are located in the C-terminal region of Amb a 1. Therefore the alpha and beta chains were designed to include these relevant T cell epitopes.

EXAMPLES Example 1 Isolation of a cDNA Coding for Amb a 1 Example 1.1 Affinity Purification of Rabbit Anti-Amb a 1 Antibodies

Sera from rabbits immunized with natural Amb a 1 can be obtained by general methods known in the art. For screening the ragweed pollen cDNA library, Amb a 1-specific antibodies were purified by affinity chromatography. 5 mg of natural Amb a 1 purified from ragweed pollen was coupled to CNBr-activated Sepharose (GE Healthcare Life Sciences). After binding of the rabbit sera, the resin was washed and highly specific Amb a 1-specific antibodies were eluted with 0.2 M glycine, pH 2.8. The antibodies were immediately neutralized and dialyzed against 1×PBS pH 7.4 (8 g NaCl, 0.2 g KCl, 1.44 g Na₂HPO₄, 0.24 g KH₂PO₄, adjust with HCl to pH 7.4). Purified antibodies were then used for immunoblotting and library screening experiments.

Example 1.2 Construction and Immunoscreening of a Ragweed Pollen cDNA Library

A ragweed pollen cDNA library was constructed in the lambda ZAP II vector (Stratagene). Purified rabbit anti-Amb a 1-antibodies were used to screen 400.000 plaques of the ragweed pollen cDNA library. Four positive Amb a 1 clones were isolated and used for in vivo excision of pBluescript phagemid from the Uni-ZAP XR vector. The clones designated R1, R2, R3 and R4 were selected for DNA sequence analysis, which was carried out by the “primer walking” technique using 4 and 5 primers including the flanking primers T7 und T3. R1 and R4 were truncated at their 3′ and 5′ ends, respectively, and therefore were not further used in the present experiments. Both strands of R2 and R3 were sequenced twice. The sequences were used for similarity searches in the Database.

Example 1.3 Cloning into Expression Vector pHis-Parallel-2

The R2 (Amb a 1.3) cDNA was ligated into the vector pHis-parallel-2. For the cloning procedure two flanking cloning primers were constructed. The complete cDNA sequence was truncated at the 5′ end by 75 nucleotides coding for the putative signal peptide. The following primers were used: Rag-Nco-forward: 5′-GAGAGAGACCATGGCCGAAGGGGTCGG-AGAAATCTTACCTTCAG-3′ (SEQ ID No. 140) and Rag-Xho-reverse: 5′-GAGAGAGACTCGAGTTAGCAAGGTGCTCCAGGACGGCATGAG-3′ (SEQ ID No. 141). Nco I and Xho I restriction sites were introduced at the 5′ and 3′ ends. The polymerase chain reaction (PCR) products were digested with Nco I and Xho I restriction enzymes (New England Biolabs) and ligated to the respective sites of the vector pHis-parallel-2. The resulting pHis-parallel-2/R2 construct was sequenced according to the Dye Terminator Cycle Sequencing protocol (Applied Biosystems).

Example 1.4 Expression of Recombinant R2 (Amb a 1.3) in Escherichia coli

Recombinant protein expression was performed using competent Escherichia coli strain BL21 DE3 (Stratagene) hosting the construct pHis-Parallel-2/R2 (for Amb a 1.3). The transformants were selected on LB plates containing 100 mg/L ampicillin and single transformant colonies were picked. Several small-scale expression experiments were carried out and optimized before attempting a large-scale protein production. The culture medium (10 g/L peptone, 5 g/L yeast extract, 10 g/L glycerol, 5 g/L NaCl, 2.5 g/L (NH₄)₂SO₄, 0.5 g/L MgSO₄.7H₂O and 1.8 g/L Na₂HPO₄.2H₂O, pH adjusted to 7.4) was inoculated with 3% of an overnight culture, grown in culture medium with 150 μg/mL penicillin G (Biochemie). Fermentation was carried out in a 10 L Bioflow 3000 Fermenter (New Brunswick Scientific Co.) at 37° C. with 7% oxygen saturation 200-400 rpm agitation and induction with 0.4 mM IPTG at an OD₆₀₀ of 1.0. Bacterial cells (60-80 g wet cell weight from 10 L culture) were harvested by centrifugation 3 hours post induction and resuspended in 100 mL 50 mM Tris base, 1 mM EDTA, 0.1% Triton X-100 (pH unadjusted, 5 mL/g cells). After addition of freshly dissolved lysozyme (100 μg/g cells) and incubation at room temperature for 1 hour, the cells were lysed by 3 freeze-thaw cycles. Separation of the soluble fraction was done by centrifugation and the raw inclusion bodies were washed two to three times with 1% Triton X-100, 20 mM Tris-HCl pH 8.0, 1 mM EDTA, followed by 2 washes with 50% ethanol, 20 mM Tris-HCl pH 8.0. Purified inclusion bodies were dissolved in 500 mL 8 M urea, 0.5 M NaCl, 20 mM Tris-HCl pH 8.0.

Example 1.5 Purification of Recombinant R2 (Amb a 1.3) Allergen

The solution was loaded on a 150 mL Chelating Cellufine Column (Millipore) pre-equilibrated with the buffer described in the last step, after charging it with NiCl₂ according to the manufacturers' instructions. All chromatography steps were carried out on a Biopilot FPLC system (GE Healthcare Life Sciences). Bound protein was eluted with a linear imidazole gradient ranging from 0-300 mM. The purity of the fractions was analyzed by conventional SDS-PAGE. Fractions containing nearly pure Amb a 1.3 were stabilized with 2 mM EDTA and prepared for the following gel filtration step by concentration to a volume of 50 mL in a Vivaflow 50 ultrafiltration cell (Vivascience). Gel filtration was performed in 8 M urea, 0.5 M NaCl, 20 mM Tris-HCl pH 8.0, 2 mM EDTA on a Sephacryl S-200 HR (GE Healthcare Life Sciences) column (dimensions 50×1000 mm). Pure Amb a 1 fractions were again concentrated to a protein concentration of approximately 3 mg/mL by ultrafiltration. Before lyophilization a refolding procedure was performed, in which disulfide bonds were reduced by addition of 10 mM mercaptoethanol and re-oxidized during subsequent dialysis against the 1,000-2,000-fold volume of 5 mM NH₄HCO₃ at 4° C.

Example 1.6 SDS-PAGE and Immunoblot Analysis of the Purified Recombinant Amb a 1.3

The proteins were analyzed via SDS-PAGE using 15% acrylamide gels and 0.1% Coomassie staining with a molecular weight standard RPN 756 (GE Healthcare Life Sciences). Sera from allergic patients were tested for positive IgE-reactivity. rAmb a 1 and rArt v 6 were separated on 15% (w/w) polyacrylamide gels and electroblotted onto a PVDF membrane. After blocking the non-specific protein binding sites with Blocking buffer (per L: 7.5 g Na₂HPO₄, 1 g NaH₂PO₄, 5 g BSA and 5 mL Tween 20), the membrane was incubated with patients' sera (diluted 1:10 in Blocking buffer) for more than 6 hours at room temperature. The membrane was washed for at least 30 minutes with Blocking buffer before it was incubated with radiolabeled [¹²⁵I]-anti human IgE (RAST, 5 □Ci, MedPro) diluted in Blocking buffer (1:40) overnight at room temperature. After a second 30-minute wash, the membrane was placed onto an imaging plate. The screen was exposed for at least 24 hours and developed using a PhosphoImager Bas-1800 II scanner for detection and the instrument's supporting software (Fujifilm).

Example 1.7 cDNA Clones Coding for Amb a 1 Isoforms

The R2 and R3 clones isolated from the ragweed pollen library were complete and coded for Amb a 1 isoforms. The deduced amino acid sequence of R3 differed from the mature Amb a 1.1 isoform in one amino acid: glycine at position 50 of mature Amb a 1.1 is exchanged for an alanine in R3. The deduced amino acid sequence of R2 is identical to Amb a 1.3 isoform. The R2 clone was used for all experiments described here and will be referred to as Amb a 1.3.

Example 1.8

Recombinant Production and IgE Binding Activity of Amb a 1.3

In terms of IgE-binding activity, the first attempts to produce full-length rAmb a 1.3 in E. coli were not encouraging. First of all, proteolytic cleavage occurred during the purification of rAmb a 1.3 produced in E. coli. The yield of rAmb a 1.3 was approximately 15 mg rAmb a 1.3 from 10 L fermentation culture. rAmb a 1.3 was found exclusively in inclusion bodies and therefore the use of protocols for refolding were necessary. However, the correct refolding of full-length rAmb a 1.3 turned out to be a hurdle. After using different standard procedures for refolding, the best preparations consisted mostly of insoluble aggregates (see FIG. 1).

Various changes in the purification protocol and addition of different stabilizing agents did not result in a correctly folded and soluble protein. In non-denaturing assays (e.g., dot blot, ELISA) rAmb a 1.3 was not able to bind human IgE (FIG. 2). Only after reduction and heat treatment (standard procedure for SDS-PAGE/immunoblotting) rAmb a 1.3 reacted with patients IgE. These results clearly demonstrated that rAmb a 1.3 produced as described above is not a suitable reagent for allergy diagnosis and therapy. Thus, another approach for producing recombinant reagents with full IgE-binding activity was pursued, as described in section 4. Despite its low IgE-binding activity, rAmb a 1.3 was successfully used in vitro for T cell epitope mapping and proliferation assays, as correct folding is not essential for T cell recognition (see example 2).

Example 2 T Cell Recognition of Amb a 1 Example 2.1 Patients

The T cell response to Amb a 1 was characterized in detail using the established in vitro culture system (Jahn-Schmid et al., J. Immunol. 169: 6005-11, 2002; Jahn-Schmid et al., J. Allergy Clin. Immunol., 115: 399-404, 2005). In total, 85 clinically well-defined patients (75 from Vienna/10 from Milano) with typical case history, positive skin prick test and CAP/RAST tests for ragweed extract were included.

Example 2.2 PBMC, Amb a 1-Specific T Cell Lines (TCL) and T Cell Clones (TCC)

Peripheral blood mononuclear cells (PBMC) were isolated from heparinized blood of allergic patients by Ficoll density gradient centrifugation. To generate allergen-specific T cell lines (TCL) and T cell clones (TCC), 1.5×106 PBMC were stimulated with optimal doses of ragweed or mugwort extract (4 μg/ml) or rAmb a 1.3 (10 μg/ml) in 24-well flat-bottomed culture plates (Costar, USA). After 5 days human rIL-2 (10 U/ml, Boehringer, Mannheim, Germany) were added and cultures were continued for additional 7 days. Then, T cell blasts were isolated by density centrifugation. The majority of T cell blasts was further expanded with IL-2 and irradiated PBMC. A small number of T cell blasts were used to establish monoclonal T cell cultures by limiting dilution: 0.3 T cells/well were seeded into 96 well round bottom plates (Nunclone) in the presence of 2×10⁵ irradiated (60 Gy) PBMC, 0.25% v/v PHA (Gibco, USA) and rIL-2 (4 U/well) in the medium mentioned above. After 14-21 days, growing microcultures were expanded at weekly intervals with irradiated PBMC and rIL-2. The specificity of TCC was assessed in proliferation assays using irradiated allogeneic or HLA-matched PBMC or irradiated EBV-transformed allogeneic B-cells and 5 μg/ml Amb a 1.3. After 48 hours, cellular uptake of tritiated (³H)-thymidine was performed to measure proliferation in counts per minute (cpm). When the stimulation index (SI; ratio between cpm obtained in cultures containing TCC plus autologous APC plus antigen, and cpm obtained in cultures containing TCC and APC alone) was >10, responses were considered as positive. Allergen-specific TCC were expanded by alternating turns of stimulation with autologous irradiated APC and allergen or with allogeneic feeder cells and rIL-2. For PBMC and TCL, which showed different degrees of background proliferation due to autoreactivity, an SI of >3 or respectively 10.000 dpm were considered as cut-off for antigen-specificity.

Amb a 1-specific TCL and TCC were used to identify T cell epitopes of Amb a 1.3. T cell cultures were stimulated with a panel of 121 synthetic 12-mer peptides and one 13-mer representing the C-terminal peptide of Amb a 1.3 (Pepset, Biotrend, Germany). Peptides had been synthesized according to the Amb a 1.3 amino acid sequence and overlapped for 9 amino acid residues with the neighbouring peptides (Table 1). Peptides were used at a concentration of 5 μg/ml for stimulation and proliferation of T cell cultures was determined after 48 hrs by ³H-thymidine-uptake. Because of the frequently observed high background caused by auto-reactivity in TCL, the mean of the cpm observed with the ten least stimulating peptides (none of the peptides was toxic) was used as negative control in calculations of SI. Throughout this manuscript, a peptide comprised one T cell epitope when the stimulation index was at least 3.0. Stronger stimulating peptides with SI≧5.0 are also indicated in Tables 2 and 3.

TABLE 1 Synthetic peptides used for T cell epitope mapping of Amb a 1.3. Deduced amino acid sequence of mature (without signal peptide) Amb a 1.3 was used as template to design 120 12-mer plus 1 13-mer peptide (corresponding to C-terminus of Amb a 1.3). Pept # (=SEQ Aa pos. ID No.) Sequence 25-36 1 SAEGVGEILPSV 28-39 2 GVGEILPSVNET 31-42 3 EILPSVNETRSL 34-45 4 PSVNETRSLQAC 37-48 5 NETRSLQACEAY 40-51 6 RSLQACEAYNII 43-54 7 QACEAYNIIDKC 46-57 8 EAYNIIDKCWRG 49-60 9 NIIDKCWRGKAD 52-63 10 DKCWRGKADWEN 55-66 11 WRGKADWENNRQ 58-69 12 KADWENNRQALA 61-72 13 WENNRQALADCA 64-75 14 NRQALADCAQGF 67-78 15 ALADCAQGFAKG 70-81 16 DCAQGFAKGTYG 73-84 17 QGFAKGTYGGKW 76-87 18 AKGTYGGKWGDV 79-90 19 TYGGKWGDVYTV 82-93 20 GKWGDVYTVTSN 85-96 21 GDVYTVTSNLDD 88-99 22 YTVTSNLDDDVA  91-102 23 TSNLDDDVANPK  94-105 24 LDDDVANPKEGT  97-108 25 DVANPKEGTLRF 100-111 26 NPKEGTLRFAAA 103-114 27 EGTLRFAAAQNR 106-117 28 LRFAAAQNRPLW 109-120 29 AAAQNRPLWIIF 112-123 30 QNRPLWIIFKND 115-126 31 PLWIIFKNDMVI 118-129 32 IIFKNDMVINLN 121-132 33 KNDMVINLNQEL 124-135 34 MVINLNQELVVN 127-138 35 NLNQELVVNSDK 130-141 36 QELVVNSDKTID 133-144 37 VVNSDKTIDGRG 136-147 38 SDKTIDGRGVKV 139-150 39 TIDGRGVKVEII 142-153 40 GRGVKVEIINGG 145-156 41 VKVEIINGGLTL 148-159 42 EIINGGLTLMNV 151-162 43 NGGLTLMNVKNI 154-165 44 LTLMNVKNIIIH 157-168 45 MNVKNIIIHNIN 160-171 46 KNIIIHNINIHD 163-174 47 IIHNINIHDVKV 166-177 48 NINIHDVKVLPG 169-180 49 IHDVKVLPGGMI 172-183 50 VKVLPGGMIKSN 175-186 51 LPGGMIKSNDGP 178-189 52 GMIKSNDGPPIL 131-192 53 KSNDGPPILRQA 184-195 54 DGPPILRQASDG 187-198 55 PILRQASDGDTI 190-201 56 RQASDGDTINVA 193-204 57 SDGDTINVAGSS 196-207 58 DTINVAGSSQIW 199-210 59 NVAGSSQIWIDH 202-213 60 GSSQIWIDHCSL 205-216 61 QIWIDHCSLSKS 208-219 62 IDHCSLSKSFDG 211-222 63 CSLSKSFDGLVD 214-225 64 SKSFDGLVDVTL 217-228 65 FDGLVDVTLGST 220-231 66 LVDVTLGSTHVT 223-234 67 VTLGSTHVTISN 226-237 68 GSTHVTISNCKF 229-240 69 HVTISNCKFTQQ 232-243 70 ISNCKFTQQSKA 235-246 71 CKFTQQSKAILL 238-249 72 TQQSKAILLGAD 241-252 73 SKAILLGADDTH 244-255 74 ILLGADDTHVQD 247-258 75 GADDTHVQDKGM 250-261 76 DTHVQDKGMLAT 253-264 77 VQDKGMLATVAF 256-267 78 KGMLATVAFNMF 259-270 79 LATVAFNMFTDN 262-273 80 VAFNMFTDNVDQ 265-276 81 NMFTDNVDQRMP 268-279 82 TDNVDQRMPRCR 271-282 83 VDQRMPRCRFGF 274-285 84 RMPRCRFGFFQV 277-288 85 RCRFGFFQVVNN 280-291 86 FGFFQVVNNNYD 283-294 87 FQVVNNNYDRWG 286-297 88 VNNNYDRWGTYA 289-300 89 NYDRWGTYAIGG 292-303 90 RWGTYAIGGSSA 295-306 91 TYAIGGSSAPTI 293-309 92 IGGSSAPTILCQ 301-312 93 SSAPTILCQGNR 304-315 94 PTILCQGNRFLA 307-318 95 LCQGNRFLAPDD 310-321 96 GNRFLAPDDQIK 313-324 97 FLAPDDQIKKNV 316-327 98 PDDQIKKNVLAR 319-330 99 QIKKNVLARTGT 322-333 100 KNVLARTGTGAA 325-336 101 LARTGTGAAESM 328-339 102 TGTGAAESMAWN 331-342 103 GAAESMAWNWRS 334-345 104 ESMAWNWRSDKD 337-348 105 AWNWRSDKDLLE 340-351 106 WRSDKDLLENGA 343-354 107 DKDLLENGAIFV 346-357 108 LLENGAIFVTSG 349-360 109 NGAIFVTSGSDP 352-363 110 IFVTSGSDPVLT 355-366 111 TSGSDPVLTPVQ 358-369 112 SDPVLTPVQSAG 361-372 113 VLTPVQSAGMIP 364-375 114 PVQSAGMIPAEP 367-378 115 SAGMIPAEPGEA 370-381 116 MIPAEPGEAAIK 373-384 117 AEPGEAAIKLTS 376-387 118 GEAAIKLTSSAG 379-390 119 AIKLTSSAGVLS 382-393 120 LTSSAGVLSCRP 385-397 121 SAGVLSCRPGAPC

Example 2.3 Measurement of Cytokines

T cells were washed and incubated with irradiated autologous APC in the presence of the stimulant (5 μg/ml) for 48 hours. Cytokine levels in the resulting supernatants were measured in ELISA using matched antibody pairs (Endogen, USA) (sensitivity limits: IL-4: 9 μg/ml, IFN-γ: 9 μg/ml). Cultures containing TCC and APC alone served as negative controls. TCC with a ratio of IFN-γ/IL-4>10 were classified as Th1, 0.1-10 as Th0 and <0.1 as Th2.

Example 2.4 Flow Cytometry

The phenotype of TCC was analyzed by flow cytometry, using a FACScan and the FITC-labeled monoclonal antibodies anti-Leu4/CD3, anti-Leu 3a/CD4, anti-Leu 2a/CD8, anti-TCR αβ WT 31, anti-TCR γδ and CRTh2 plus goat-anti-rat-PE (all antibodies were obtained from BD Bioscience, USA).

Example 2.5 Comparison of rAmb a 1.3 with Natural Amb a 1

To confirm that recombinant Amb a 1.3 isoform stimulated T cells comparable to natural Amb a 1 (mixture of isoforms), PBMC and Amb a 1-specific TCL and TCC were stimulated with different concentrations of natural or rAmb a 1.3. Proliferation and cytokine responses were determined. The stimulatory capacity of both allergens was relatively stable over a range of concentrations and in general natural and rAmb a 1.3 induced comparable T cell proliferations (FIGS. 3 and 4) and cytokine production (FIGS. 5 and 6). At the clonal level 1/6 tested Amb a 1-specific TCC recognizing different epitopes of rAmb a 1.3 did not respond to natural Amb a 1 (epitope: aa 265-276). TCL induced with ragweed extract or recombinant Amb a 1.3 showed similar T cell epitope patterns (FIG. 7).

Example 2.6 T Cell Epitopes of Amb a 1.3

T cell epitope mapping of Amb a 1.3 was performed evaluating 48 TCL from different patients (37 from Vienna and 9 from Italy), which had been initiated with ragweed extract (containing the natural allergen) or rAmb a 1.3 (Table 2). TCL induced with either ragweed extract or rAmb a 1.3 from the same individual recognized similar T cell epitopes (Table 2; FIG. 7). Austrian and Italian patients showed a similar epitope recognition profile. Therefore, their data were combined for further analysis (Table 3). Typical for many inhalant allergens, multiple T cell activating regions were detected in Amb a 1.3. The number of peptides recognized by T cells from a single individual ranged from 2 to maximum 60 peptides with a mean of 17.8 peptides (median=16/for SI>3; resp. 0-36/11.9/12 for SI>5) (see Table 3). In total, 26 relevant (i.e. recognized by ≧10% of patients studied) T cell activating regions comprising 12-18 aa were identified. These epitope-containing regions were divided into classes of prevalence (referring to SI>5):

11 regions were positive in 10-20% of patients:

Peptide 20 (aa 82-93), (SEQ ID No. 20) GKWGDVYTVTSN, recognized by 14.6% 42; (aa 148-159), (SEQ ID No. 42) EIINGGLTLMNV, recognized by 10.4% 44 (aa 154-165), (SEQ ID No. 44) LTLMNVKNIIIH, recognized by 18.8% 78; (aa 256-267), (SEQ ID No. 78) KGMLATVAFNMF, recognized by 12.5% 80-81 (aa 262-276), (SEQ ID No. 122) VAFNMFTDNVDQRMP, recognized by 12.5% 83; (aa 271-282), (SEQ ID No. 83) VDQRMPRCRFGF, recognized by 16.7% 88-89: (aa 286-300), (SEQ ID No. 123) VNNNYDRWGTYAIGG, recognized by 12.5% 94 (aa 304-315), (SEQ ID No. 94) PTILCQGNRFLA, recognized by 18.8% 98-99; (aa 316-330), (SEQ ID No. 124) PDDQIKKNVLARTGT, recognized by 16.7% 100; (aa 322-333). (SEQ ID No. 100) KNVLARTGTGAA, recognized by 10.4% 101/102 (aa 325-339), (SEQ ID No. 125) LARTGTGAAESMAWN, recognized by 14.6% 9 regions were positive in 21-30% of patients:

Peptide 27-28 (aa103-117), (SEQ ID No. 126) EGTLRFAAAQNRPLW, recognized by 22.9% 30-31 (aa112-126), (SEQ ID No. 127) QNRPLWIIFKNDMVI, recognized by 20.8% 33-34 (aa 121-135), (SEQ ID No. 128) KNDMVINLNQELVVN, recognized by 27.1% 36-37 (aa 130-144), (SEQ ID No. 129) QELVVNSDKTIDGRG, recognized by 25.0% 46-48 (aa 160-177), (SEQ ID No. 130) KNIIIHNINIHDVKVLPG, recognized by 20.8% 86; (aa 280-291), (SEQ ID No. 86) FGFFQVVNNNYD, recognized by 20.6% 91 (aa 295-306), (SEQ ID No. 91) TYAIGGSSAPTI, recognized by 22.9% 109-111; (aa 349-366), (SEQ ID No. 131) NGAIFVTSGSDPVLTPVQ, recognized by 22.9% 118-120 (aa 376-393); (SEQ ID No. 132) GEAAIKLTSSAGVLSCRP, recognized by 20.8% 3 regions were positive in 31-49% of patients:

Peptide 38-40 (aa 136-153), (SEQ ID No. 133) SDKTIDGRGVKVEIINGG, recognized by 33.3% 68 (aa 226-237), (SEQ ID No. 68) GSTHVTISNCKF, recognized by 33.3% 114-115 (aa 364-378), (SEQ ID No. 134) PVQSAGMIPAEPGEA, recognized by 35.4% 3 regions were positive in >50% of patients:

Peptide 52 (aa 178-189), (SEQ ID No. 52) GMIKSNDGPPIL, recognized by 56.3% 59-61 (aa 199-216), (SEQ ID No. 135) NVAGSSQIWIDHCSLSKS, recognized by 58.3% 107-108 (aa 343-357), (SEQ ID No. 136) DKDLLENGAIFVTSG, recognized by 56.3%

The three T cell activating regions inducing proliferative responses in more than 50% of the allergic patients were defined as immunodominant epitopes (FIG. 8; Table 3).

In general, the T cell activating capacity of a certain peptide did not correlate with the frequency of recognition. Therefore, also a “positivity index” (PI; % positive patients x mean SI) was calculated to reveal other important epitopes. PI ranged from 98-2300 and identified the three immunodominant regions mentioned above and 4 additional regions as strongly immunogenic regions (PI>700; 27% highest values) in Amnb a 1.3:

46-48: aa 160-177: (SEQ ID No. 130) KNIIIHNINIHDVKVLPG 109-111: aa 349-366: (SEQ ID No. 131) NGAIFVTSGSDPVLTPVQ 114-115: aa 364-378: (SEQ ID No. 134) PVQSAGMIPAEPGEA 118-120: aa 376-393: (SEQ ID No. 132) GEAAIKLTSSAGVLSCRP

In addition to TCL, more than 100 Amb a 1-specific TCC from 10 different ragweed pollen-allergic patients was established. With the exception of one CD8+TCC, these TCC were shown to be CD4′TCR αβ* T cells. Investigation of the cytokine production in 108 Amb a 1-specific TCC (n-10 patients) revealed a Th2-like cytokine profile in the majority (50%) of these TCC (Th1: 11%; Th0 39%). In addition, 74% of 68 investigated TCC (patients n=8) expressed CRTh2, a surface marker for Th2 T cells also indicating that Amb a 1-specific T cells in our culture represent relevant allergenic T cells. T cell epitope mapping of Amb a 1.3 using Amb a 1-specific TCC reflected the data obtained from TCL. Results show that the presentation of Amb a 1-peptides is diverse, involving HLA-DR, -DP or -DQ as restriction elements.

In the U.S. Pat. No. 6,335,020 (Allergenic peptides from ragweed pollen) 4 major regions of T cell reactivity have been reported: aa 57-101, 182-215, 280-322 and 342-377 (FIG. 6). This epitope distribution differs to some extent from the epitopes of the present invention, e.g. in contrast to region aa 57-101, it was found that epitopes within aa 109-180 are much more frequently recognized. T cell epitopes from related tree pollen allergens Cha o 1 (Japanese cypress), Cry j L (Japanese cedar) have been described by others (Sone et al., Clin Exp Allergy, 35: 664-71, 2005). The major epitopes of these allergens are located in regions that are homologous to minor T cell epitopes in Amb a 1.

TABLE 2 T cell epitopes of Amb a 1-specific TCL from 48 different ragweed pollen-allergic patients. TCL were initiated either with rAmb a 1.3 or with ragweed pollen extract. Peptides giving Stimulation indexes (SI) higher than 3 and 5 are listed for each patient. Patient No. Peptide No. (SI >3) Peptide No. (SI >5) 1 112, 114 8, 31, 33, 36, 44, 52, 59, 60, 61, 68, 78, 102, 108, 109, 110, 111, 115, 116, 117, 118, 119, 120 2 29, 30, 42, 64, 67, 27, 28, 33, 52, 60, 61, 79, 88, 89, 93, 98, 68, 94, 107, 108, 111, 101, 103 114, 115, 116, 118, 119, 120 3 120 107 4 41, 42, 60, 90, 98 52, 83, 91, 107, 108 5 39, 78, 85, 99, 101, 28, 36, 37, 44, 52, 60, 102, 107, 108 61, 86, 100, 104, 105, 106, 109, 110, 111, 119, 120 6 34 83, 91, 107, 108, 115 7 11, 58, 68, 78, 82, 33, 39, 47, 48, 51, 52, 84, 86, 88, 89, 99, 59, 60, 61, 107 108 8 34, 44, 45, 72, 79, 33, 39, 40, 71, 83 80 107 9 50, 76, 83, 87, 101, 39, 69, 91, 93, 107, 112, 113, 119, 121 117 10 47, 96, 97, 110, 119 44, 46, 60, 61, 69, 89, 101, 107, 108, 115 11 110 33, 38, 39, 16, 52, 60, 69, 83, 90, 91, 107, 108, 115 12 59 36, 37, 52, 60, 61, 68, 86, 96, 97, 98 13 14, 37, 44, 61, 71, 20, 28, 36, 47, 101, 77, 108, 111, 121 109, 110, 118 14 30, 31, 111, 120, 119 15 8, 20, 46, 47, 71, 77, 107, 108 16 87 21, 46, 47, 54, 55, 63, 86 17 14, 23, 29, 34, 53, 20, 22, 28, 31, 33, 36, 58, 69, 76, 80, 82, 37, 44, 52, 60, 61, 68, 85, 99, 102, 107, 77, 81, 84, 88, 98, 115, 108, 109, 110, 111, 118, 119, 120 18 33, 104 38, 39, 52, 60, 61, 68, 81, 96, 97, 98, 107, 108, 112 19 20, 28, 36, 37, 44, 47, 48, 52, 59, 60, 67, 77, 78 20 60, 61 21 29, 34, 47, 61 30, 33, 38, 39, 42, 43, 46, 49, 52, 60, 91, 94, 107, 108, 114, 115 22 20, 39, 44, 52, 53, 28, 37, 38, 40, 60, 61, 64, 69, 85, 94 68, 86 23 23, 51, 53, 54, 55, 9, 30, 31, 32, 33, 34, 59, 116, 117, 120, 38, 39, 46, 47, 48, 52, 60, 61, 68, 81, 88, 89, 98, 99, 107, 108, 111, 115, 118, 119 24 28, 114 11, 34, 37, 38, 52, 68, 83, 89, 91, 100, 101, 102, 107, 108, 109, 110, 115 25 44, 111, 119, 120 60, 61, 77, 92, 93, 94107, 108, 109, 110 26 28, 29, 30, 36, 44, 12, 15, 22, 23, 31, 33, 68, 83, 84, 118, 121 52, 60, 61, 73, 74, 78, 82, 86, 107, 108, 111, 113, 115, 119, 120 27 43, 107 10, 22, 28, 30, 33, 36, 37, 48, 52, 60, 61, 86, 87 28 33, 39, 61, 73, 93, 36, 52, 60, 77, 88, 94, 99, 118 102, 107, 108, 109, 110, 111, 119, 120 29 28, 81, 83, 86, 87, 31, 39, 52, 59, 60, 61, 91, 100 67, 68, 69, 80, 107, 108, 111, 115, 118, 119, 120 30 4, 78 20, 27, 28, 29, 30, 36, 37, 44, 52, 60, 61, 68, 80, 93, 94, 108, 117 31 11, 32, 77 29, 30, 38, 39, 40, 42, 46, 47, 48, 61, 79, 89, 94, 108, 115 32 1, 77 4, 20, 22, 28, 36, 37, 38, 39, 41, 42, 44, 50, 52, 60, 61, 62, 66, 68, 78, 83, 36, 90, 91, 96, 97, 98, 105, 107, 108, 115 33 12, 61 52, 60, 68, 108 34 28, 30, 42, 91 24, 27, 29, 94, 108, 114 35 37, 38, 69, 72 20, 28, 33, 36, 39, 42, 44, 48, 52, 58, 60, 61, 68, 94, 114 36 7, 9, 12, 15, 16, 30, 52, 60, 61, 68, 96, 28, 33, 37, 39, 43, 97, 98, 107 47 37 5, 12, 29, 55, 59 38 19, 37, 39, 41, 42, 20, 22, 28, 31, 36, 44, 43, 15, 46, 47, 48, 52, 78, 82, 86, 89, 90, 49, 51, 98, 107, 101, 102, 110, 111, 109, 113 118, 119, 120 39 4, 52 33, 42, 47, 48, 59, 60, 78, 98, 99, 107 40 24, 25, 33, 52, 73, 31, 66, 68, 71, 80, 81, 78, 98, 109, 111, 83, 102, 107, 108, 110, 119 112, 115, 120 41 2, 17, 20, 28, 30, 27, 31, 39, 52, 83, 91, 36, 37, 38, 44, 61, 94 92 42 67, 80 91, 93, 101 43 28, 62, 68, 76, 88, 38, 39, 51, 52, 59, 60, 89 61, 80, 81, 86, 92, 100, 101, 102, 109, 110 44 35, 80, 88, 90, 119 30, 31, 38, 39, 46, 47, 48, 51, 52, 59, 60, 94, 100, 107, 108, 111, 112, 115, 121 45 5, 39, 41, 42, 48, 47, 60, 61, 63, 64, 66, 51, 52, 53, 54, 65, 72, 73, 75, 76, 80, 85, 67, 68, 74, 78, 79, 86, 87, 88, 101, 107, 84, 89, 106, 109, 108, 115, 116 112 46 88 27, 91, 107 47 3, 4, 5, 6, 13, 14, 2, 9, 15, 30, 50, 56, 16, 23, 28, 41, 49, 62, 91, 99, 100, 103, 61, 74, 89, 98, 102, 105, 107, 110, 111, 108, 112, 113, 114, 115, 117 116, 119, 120, 121 48 1, 5, 8, 12, 13, 14, 10, 11, 10, 30, 31, 33, 15, 18, 19, 20, 21, 38, 39, 40, 46, 47, 48, 25, 32, 36, 42, 53, 49, 50, 52, 54, 59, 60, 65, 67, 69, 88, 97, 61, 66, 68, 70, 72, 79, 105, 106, 111 80, 81, 89, 98, 99, 107, 108, 109, 114, 115, 116, 118, 121

TABLE 3 T cell epitopes of Amb a 1-specific T cell lines (TCL) from 48 different ragweed pollen-allergic patients (see Table 2). 121 overlapping synthetic peptides (12-mer) were used for epitope mapping. The relevance of each epitope was separately evaluated for stimulation indexes higher than 3 (SI > 3) and higher than 5 (SI > 5). Peptide No. positive No. positive (=SEQ ID AA AA patients patients No.) position sequence SI > 3 % SI > 5 % 1 25-36 SAEGVGEILPSV 2 4.2 0 0.0 2 20-39 GVGEILPSVNET 2 4.2 1 2.1 3 31-42 EILPSVNETRSL 1 2.1 0 0.0 4 34-45 PSVNETRSLQAC 4 8.3 1 2.1 5 37-48 NETRSLQACEAY 4 8.3 0 0.0 6 40-51 RSLQACEAYNII 1 2.1 0 0.0 7 43-54 QACEAYNIIDKC 1 2.1 0 0.0 8 46-57 EAYNIIDKCWRG 3 6.3 1 2.1 9 49-60 NIIDKCWRGKAD 3 6.3 2 4.2 10 52-63 DKCWRGKADWEN 2 4.2 2 4.2 11 55-66 WRGKADWENNRQ 4 8.3 2 4.2 12 58-69 KADWENNRQALA 5 10.4 1 2.1 13 61-72 WENNRQALADCA 2 4.2 0 0.0 14 64-75 NRQALADCAQGF 4 8.3 0 0.0 15 67-78 ALADCAQGFAKG 4 8.3 2 4.2 16 70-81 DCAQGFAKGTYG 2 4.2 0 0.0 17 73-84 QGFAKGTYGGKW 2 4.2 1 2.1 18 76-87 AKGTYGGKWGDV 1 2.1 0 0.0 19 79-90 TYGGKWGDVYTV 2 4.2 0 0.0 20 82-93 GKWGDVYTVTSN 9 18.8 7 14.6 21 85-96 GDVYTVTSNLDD 2 4.2 1 2.1 22 88-99 YTVTSNLDDDVA 4 8.3 4 8.3 23  91-102 TSNLDDDVANPK 2 4.2 1 2.1 24  94-105 LDDDVANPKEGT 2 4.2 1 2.1 25  97-108 DVANPKEGTLRF 2 4.2 0 0.0 26 100-111 NPKEGTLRFAAA 0 0.0 0 0.0 27 103-114 EGTLRFAAAQNR 5 10.4 5 10.4 28 106-117 LRFAAAQNRPLW 15 31.3 11 22.9 29 109-120 AAAQNRPLWIIF 4 8.3 3 6.3 30 112-123 QNRPLWIIFKND 11 22.9 9 18.8 31 115-126 PLWIIFKNDMVI 11 22.9 10 20.8 32 118-129 IIFKNDMVINLN 2 4.2 1 2.1 33 121-132 KNDMVINLNQEL 15 31.3 13 27.1 34 124-135 MVINLNQELVVN 2 4.2 2 4.2 35 127-138 NLNQELVVNSDK 1 2.1 1 2.1 36 130-141 QELVVNSDKTID 14 29.2 12 25.0 37 133-144 VVNSDKTIDGRG 14 29.2 9 18.8 38 136-147 SDKTIDGRGVKV 13 27.1 11 22.9 39 139-150 TIDGRGVKVEII 19 39.6 16 33.3 40 142-153 GRGVKVEIINGG 3 6.3 4 8.3 41 145-156 VKVEIINGGLTL 5 10.4 1 2.1 42 148-159 EIINGGLTLMNV 11 22.9 5 10.4 43 151-162 NGGLTLMNVKNI 4 8.3 1 2.1 44 154-165 LTLMNVKNIIIH 15 31.3 9 18.8 45 157-168 MNVKNIIIHNIN 2 4.2 0 0.0 46 160-171 KNIIIHNINIHD 10 20.8 8 16.7 47 163-174 IIHNINIHDVKV 14 29.2 10 20.8 48 166-177 NINIHDVKVLPG 10 20.8 9 18.8 49 169-180 IHDVKVLPGGMI 3 6.3 2 4.2 50 172-183 VKVLPGGMIKSN 5 10.4 4 8.3 51 175-186 LPGGMIKSNDGP 6 12.5 3 6.3 52 178-189 GMIKSNDGPPIL 31 64.6 27 56.3 53 181-192 KSNDGPPILRQA 5 10.4 0 0.0 54 184-195 DGPPILRQASDG 4 8.3 2 4.2 55 187-198 PILRQASDGDTI 3 6.3 1 2.1 56 190-201 RQASDGDTINVA 1 2.1 1 2.1 57 193-204 SDGDTINVAGSS 0 0.0 0 0.0 58 196-207 DTINVAGSSQIW 3 6.3 1 2.1 59 199-210 NVAGSSQIWIDH 11 22.9 8 16.7 60 202-213 GSSQIWIDHCSL 30 62.5 28 58.3 61 205-216 QIWIDHCSLSKS 29 60.4 24 50.0 62 208-219 IDHCSLSKSFDG 3 6.3 2 4.2 63 211-222 CSLSKSFDGLVD 2 4.2 2 4.2 64 214-225 SKSFDGLVDVTL 3 6.3 1 2.1 65 217-228 FDGLVDVTLGST 2 4.2 1 2.1 66 220-231 LVDVTLGSTHVT 4 8.3 4 8.3 67 223-234 VTLGSTHVTISN 6 12.5 2 4.2 68 226-237 GSTHVTISNCKF 20 41.7 16 33.3 69 229-240 HVTISNCKFTQQ 8 16.7 4 8.3 70 232-243 ISNCKFTQQSKA 1 2.1 1 2.1 71 235-246 CKFTQQSKAILL 4 8.3 2 4.2 72 238-249 TQQSKAILLGAD 4 8.3 2 4.2 73 241-252 SKAILLGADDTH 4 8.3 2 4.2 74 244-255 ILLGADDTHVQD 3 6.3 1 2.1 75 247-258 GADDTHVQDKGM 1 2.1 1 2.1 76 250-261 DTHVQDKGMLAT 4 8.3 1 2.1 77 253-264 VQDKGMLATVAF 7 14.6 4 8.3 78 256-267 KGMLATVAFNMF 11 22.9 6 12.5 79 259-270 LATVAFNMFTDN 5 10.4 2 4.2 80 262-273 VAFNMFTDNVDQ 10 20.8 6 12.5 81 265-276 NMFTDNVDQRMP 7 14.6 6 12.5 82 268-279 TDNVDQRMPRCR 3 6.3 2 4.2 83 271-282 VDQRMPRCRFGF 10 20.8 8 16.7 84 274-285 RMPRCRFGFFQV 3 6.3 1 2.1 85 277-288 RCRFGFFQVVNN 4 8.3 1 2.1 86 280-291 FGFFQVVNNNYD 12 25.0 10 20.8 87 283-294 FQVVNNNYDRWG 5 10.4 2 4.2 88 286-297 VNNNYDRWGTYA 10 20.8 4 8.3 89 289-300 NYDRWGTYAIGG 11 22.9 6 12.5 90 292-303 RWGTYAIGGSSA 5 10.4 3 6.3 91 295-306 TYAIGGSSAPTI 13 27.1 11 22.9 92 298-309 IGGSSAPTILCQ 3 6.3 2 4.2 93 301-312 SSAPTILCQGNR 6 12.5 4 8.3 94 304-315 PTILCQGNRFLA 11 22.9 9 18.8 95 307-318 LCQGNRFLAPDD 0 0.0 0 0.0 96 310-321 GNRFLAPDDQIK 5 10.4 4 8.3 97 313-324 FLAPDDQIKKNV 6 12.5 4 8.3 98 316-327 PDDQIKKNVLAR 13 27.1 8 16.7 99 319-330 QIKKNVLARTGT 8 16.7 4 8.3 100 322-333 KNVLARTGTGAA 6 12.5 5 10.4 101 325-336 LARTGTGAAESM 10 20.8 7 14.6 102 328-339 TGTGAAESMAWN 9 18.8 6 12.5 103 331-342 GAAESMAWNWRS 2 4.2 1 2.1 104 334-345 ESMAWNWRSDKD 2 4.2 1 2.1 105 337-348 AWNWRSDKDLLE 4 8.3 3 6.3 106 340-351 WRSDKDLLENGA 3 6.3 1 2.1 107 343-354 DKDLLENGAIFV 30 62.5 27 56.3 108 346-357 LLENGAIFVTSG 27 56.3 24 50.0 109 349-360 NGAIFVTSGSDP 12 25.0 9 18.8 110 352-363 IFVTSGSDPVLT 13 27.1 11 22.9 111 355-366 TSGSDPVLTPVQ 16 33.3 11 22.9 112 358-369 SDPVLTPVQSAG 7 14.6 3 6.3 113 361-372 VLTPVQSAGMIP 4 8.3 1 2.1 114 364-375 PVQSAGMIPAEP 8 16.7 5 10.4 115 367-378 SAGMIPAEPGEA 18 37.5 17 35.4 116 370-381 MIPAEPGEAAIK 6 12.5 4 8.3 117 373-384 AEPGEAAIKLTS 4 8.3 3 6.3 118 376-387 GEAAIKLTSSAG 10 20.8 8 16.7 119 379-390 AIKLTSSAGVLS 16 33.3 10 20.8 120 382-393 LTSSAGVLSCRP 14 29.2 9 18.8 121 385-397 SAGVLSCRPGAPC 6 12.5 2 4.2

Example 3 Characterization of Alpha and Beta Chains of Amb a 1

nAmb a 1 undergoes spontaneously proteolysis during purification and it is cleaved into two chains, alpha and beta chain, respectively. The data using sera collected from patients in various countries (Italy, Canada and Austria) showed that most patients (90%) strongly recognized the 12-kDa beta chain. In contrast, the alpha chain weakly bound IgE antibodies of only 65% of the patients tested (FIG. 9).

In experiments aiming at the identification of T cell epitopes (described in example 2) it was found that three T cell activating regions induced proliferative responses in more than 45% of the allergic patients and were thus defined as immunodominant epitopes (Table 3, FIG. 8). Interestingly, these and other T cell activating regions are clustered in the C-terminal region of Amb a 1, which corresponds to the alpha chain. Thus, contrary to early published research (King et al. Arch. Biochem. Biophys. 212: 127-135, 1981), the present collective data show that the immunologic properties of the two Amb a 1 chains differs. These findings incited to investigate the possibility to separately produce the chains in E. coli and use them as candidate vaccine for allergy diagnosis and immunotherapy. The alpha chain with the lower IgE binding capacity but with high immunogenicity (T cell activation) is a perfect tool for specific immunotherapy whereas the highly IgE reactive beta chain is a candidate for ragweed pollen allergy diagnosis.

For this purpose, experiments to determine the exact cleavage site for the generation of the alpha and beta chains were performed, which was described for Amb a 1 during its extraction and purification from ragweed pollen (King et al. Immunochem. 11: 83-92, 1974). Besides the estimation of its molecular weight by SDS-PAGE, no structural data has been published concerning the Amb a 1 chains. Purified natural Amb a 1 (see King et al. Immunochem. 11: 83-92, 1974) was analyzed by Maldi-TOF mass spectrometry and the bands corresponding to intact, alpha and beta chains of Amb a 1 were subjected to Edman-degradation after SDS-PAGE/electroblotting/Coomassie staining. In this way, it was possible to determine the exact masses and N-terminal sequences of processed and unprocessed natural Amb a 1 (FIGS. 10-13; Table 4).

Example 3.1 N-Terminal Sequence Analysis

Natural Amb a 1 was separated by 15% SDS-PAGE and electroblotted onto polyvinyl difluoride (PVDF) membranes (Millipore). Bands corresponding to Amb a 1 and its fragments were excised, and proteins were eluted by incubation in aqueous 40% (v/v) acetonitrile and 30% (v/v) trifluoroacetic acid for 1 hour at room temperature. Samples were vacuum dried, resuspended in water, and sequenced with the HP G1005A protein sequencing system (Agilent Technologies).

Example 3.2

Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) Mass Spectrometry

The molecular peaks of sinapinic acid and bovine pancreas trypsin were used for calibration. 0.5 μl (˜0.7 μg) of purified natural Amb a 1 protein solution in the presence of 100 mM DTT and 0.5 μl of a sinapinic acid matrix were dissolved in a saturated solution of 50% (v/v) acetonitrile and 0.1% (v/v) trifluoracetic acid (TFA), mixed, and applied to the target slide. Samples were analyzed with the Kompact MALDI-TOF IV mass spectrometer (Shimadzu) in the linear flight mode.

Example 3.3 Results

Taken together, the data (FIGS. 10-13; Table 4) allowed the exact mapping of the alpha and beta chains into the deduced amino acid sequence of Amb a 1 and indicated that several proteolytic steps are involved in their generation:

(i) N-terminal sequencing of the unprocessed Amb a 1 showed that 17-20 amino acids are removed from the N-terminus of the protein.

(ii) The beta chain is 138 amino acids-long and corresponds to the N-terminal part of Amb a 1 (amino acid position 18 to 155 of the mature protein, taking Amb a 1.1 isoform as template).

(iii) The alpha chain is 207 amino acids-long and corresponds to the C-terminal part of Amb a 1 (amino acid position 165 to 371 of the mature protein, taking Amb a 1.1 isoform as template).

(iv) Nine amino acids are removed between the C-terminus of the beta chain and the N-terminus of the alpha chain.

FIG. 14 shows the deduced amino acid sequences of Amb a 1 isoforms with the putative alpha and beta chains mapped onto their sequences.

TABLE 4 Mass spectrometry analysis of natural Amb a 1 Unprocessed Amb a 1 Amb a 1 alpha chain Amb a 1 beta chain Calculated Measured Calculated Measured Calculated Measured nAmb a 1 37,832.14 21,808.54 15,086.31 22,323.24 Amb a 1.1 37,864.43 21,999.50 15,017.04 Amb a 1.2 38,625.71 22,425.10 15,268.56 Amb a 1.3 38,255.30 22,036.77 15,286.49 Amb a 1.4 38,008.93 21,953.62 15,130.29 Amb a 2 39,392.56 22,921.76 15,638.88

Example 4 Recombinant Production of Amb a 1.3 Alpha and Beta Chains Example 4.1

Construction of Expression Plasmids and Purification of Amb a 1.3 Alpha and Beta Chains Designed According to Naturally Processed Chains

Plasmid construction and purification of chains were performed as described in example 4.2. The differences in the chains are depicted in FIG. 16. Table 5 summarizes the different constructs for the recombinant production of alpha and beta chains.

Example 4.2

Recombinant Production of Modified (Version 1) Alpha and Beta Chains of Amb a 1.3

The present experiments demonstrated that the separate production of the modified chains is much more effective than the production of the full-length Amb a 1.3 molecule. The production yield of the alpha chain was approximately 100 mg/1 L fermentation culture. In addition, no significant formation of aggregates for both alpha and beta chains were observed (FIG. 18).

Example 4.2.1 Plasmid Construction

From the original R2 clone a 100 μl Standard PCR with primers designed according to the modified chains was performed. PCR products were eluted from agarose gel with Wizard Gene clean up (Promega). Both primer sets (for beta and alpha) included a NcoI site at the 5′ and a stop codon plus XhoI site at the 3′ end. With these enzymes the PCR fragments and the vector pH is parallel-2 were digested overnight at 37° C. After elution from the agarose gel (Wizard Gene clean up, Promega), the PCR fragments were ligated into the vector using a standard ligation protocol with T4 DNA ligase (Invitrogen). The ligation reaction was used to transform the bacterial strain TG1 (K12, D(lac-pro), supE, thi, hsdD5/F′ [traD36, proA+B+, lacIq, lacZDM15]) via electroporation. After plating 100 μl of the transformation, the LBamp agar plates were incubated overnight at 37° C. PCR colony screening was used to select positive clones. (Small amount of bacterial colony is used as template for standard PCR with cloning primer). Selected clones were used for 50 ml SB cultures and plasmids purification. Inserts were sequenced with ABI sequencing kit. Plasmids with correct sequence were used to transform bacterial strains BL21 and Rosetta-gami B (DE3)pLysS (Novagen). Preliminary experiments showed that higher expression levels were achieved with the Rosetta-gami B (DE3)pLysS E. coli strain (FIG. 17).

Example 4.2.2 Expression and Purification of Modified (Version 1) Amb a 1.3 Alpha and Beta Chains

10-20 clones from freshly transformed bacteria were grown in SB to OD₆₀₀ of 0.5-0.7 and then induced with 0.4 mM IPTG. The expression was performed for 4-5 h and then the culture was pelleted by centrifugation (5,000 g). Bacterial pellet was resuspended in start buffer (25 mM Na-phosphat pH 8.0; 1M NaCl). Cells were lysed by 3x freezing in liquid nitrogen and thawing at 25° C. The suspension was treated with lysozyme (5 mg/ml), Dnase (0.5 μg/ml) and sonicated for 5 minutes. After centrifugation (15,000 g) the pellets were resuspended in urea start buffer (start buffer+6M Urea+10 mM imidazole). After centrifugation (15,000 g), the supernatant was loaded onto a HisTrap Ni²⁺ column (Amersham). Elution was performed by gradient with Elution buffer (Urea start buffer+400 mM imidazole). Fractions were pooled and dialysed 3 times against 500 mM L-Arg pH 8.5. Afterwards, proteins were dialysed against PBS. Purified Amb a 1.3 alpha and beta chains (FIG. 18) were used for IgE binding and T cell proliferation assays.

Example 4.2.3 T Cell Responses to Modified (Version 1) Alpha and Beta Chains of Amb a 1.3

When compared with the results of the T cell epitope recognition in Table 3, 45/46 patients (98%) would recognize one or more epitopes in the Amb a 1 alpha-chain. Thus, the T cell responses to modified (version 1) alpha and beta chains of Amb a 1.3 was tested in proliferation assays using available Amb a 1-reactive TCL (n=6) and TCC (n=2), described in example 2.

Example 4.3

Recombinant Production

The production of alpha and beta chains designed according to naturally processed Amb a 1 were not very encouraging, with very low yields. However, data obtained from T cell epitope mapping experiments indicated that one important epitope was not included in the alpha chain, which harbours most of the T cell reactive domains (FIG. 16; aa 178-189). Therefore, new chains were designed to include this T cell epitope (Table 5, FIG. 16).

Example 4.4

IgE Binding

As shown in example 3, the naturally processed alpha and beta chains of Amb a 1 have distinct immunological properties. The alpha chain shows low IgE reactivity whereas the beta chain contains most of the IgE epitopes of Amb a 1. Therefore, to test the IgE-binding activity of the purified alpha chain, ELISA with sera from ragweed allergic patients was performed. Results from 12 patients confirmed that the alpha chain shows low/no IgE-binding activity in vitro (FIG. 19). Experiments are being carried out for the purification and characterization of the beta chain.

Example 4.5 T Cell Reactivity

Of 6 TCL tested, 2 TCL with strong reactivity to Amb a 1 are shown in FIG. 20. The alpha chain was much more effective in stimulating proliferation than the beta-chain (82% and 84% vs. 38 and 19% of the response to Amb a 1). This finding can be explained by the epitope recognition pattern of these 2 TCL (see Table 2). Two other TCL (FIG. 21) also reacted with the alpha and/or the beta chain according to their epitope profile.

2 TCC specific for epitopes within Amb a 1-alpha reacted with the alpha but not with the beta chain, albeit not as strong as with Amb a 1.3.

TABLE 5 Amb a 1.3 chains Amino Amb a 1.3 chains acid position Length Naturally processed alpha 191-397 207 amino acids beta  44-181 138 amino acids Design according to naturally alpha 191-397 208 amino acids processed beta  26-190 164 amino acids Modified (version 1) alpha 174-397 224 amino acids beta  26-173 146 amino acids Modified (version 2) alpha 174-397 224 amino acids beta  46-173 128 amino acids

SUMMARY

In summary, 26 relevant T cell activating regions of Amb a 1 were identified taking a SI>5 as threshold for positivity (FIGS. 8 and 22).

In the analysis of T cell epitopes recognized by T cell lines from 48 different patients it was found that 17/26 epitopes are located in the C-terminal region of Amb a 1.3 (alpha chain) whereas the beta chain contains only a few T cell epitopes that are mostly recognized by only 10-30% of the patients (FIG. 8, Table 3).

However, one relevant/immunodominant T cell epitope sequence recognized by more than 50% of the patients is cleaved off in the naturally occurring chains (would only partly be represented in the alpha chain). In order to cover this important T cell activating region, the invention includes the modification of the alpha chain by adding 16 amino acid residues from the C-terminus of the beta chain to the N-terminus of the alpha chain (modified version 1; FIG. 16, Table 5). Thus, the modified (version 1) construct of the Amb a 1.3 alpha chain includes the 3 most frequently recognized T cell epitopes of Amb a 1 (FIG. 22).

The use of the entire alpha chain of Amb a 1.3 (modified version 1) as a vaccine for ragweed pollen-allergy would cover 100% of the patients tested (n=48).

The use of a combination of the three immunodominant T cell epitopes identified here for peptide immunotherapy of ragweed pollen-allergic patients would cover 93% of the patients:

(Peptide 52; SEQ ID No. 52) GMIKSNDGPPIL (Peptide 60-61; SEQ ID No. 137) GSSQIWIDHCSLSKS (Peptide 107-111; SEQ ID No. 138) DKDLLENGAIFVTSGSDPVLTPVQ

The following mixture of 4 peptides would cover 95.8% of the patients:

(Peptide 52; SEQ ID No. 52) GMIKSNDGPPIL (Peptide 60-61; SEQ ID No. 137) GSSQIWIDHCSLSKS (Peptide 107-111; SEQ ID No. 138) DKDLLENGAIFVTSGSDPVLTPVQ (Peptide 119-120; SEQ ID No. 139) AIKLTSSAGVLSCRP

The addition of the following frequently recognized peptides to this optimum peptide combination could also be considered:

(Peptide 46-48; SEQ ID No. 130) KNIIIHNINIHDVKVLPG (Peptide 68; SEQ ID No. 68) GSTHVTISNCKF (Peptide 115; SEQ ID No. 115) SAGMIPAEPGEA 

1. A ragweed pollen allergen Amb a 1 peptide consisting of the amino acid sequence of SEQ ID NO: 115 or variants thereof differing by one amino acid residue or comprising conservative changes.
 2. A pharmaceutical composition, comprising a peptide according to claim
 1. 3. The pharmaceutical composition of claim 2, further comprising at least one pharmaceutically acceptable adjuvant, excipient, or carrier. 